Mercurial > repos > bgruening > diffbind
annotate diffbind.xml @ 18:f907216064f6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
author | iuc |
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date | Mon, 08 Jul 2024 18:31:51 +0000 |
parents | 2605cbdaa7d8 |
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2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
16
diff
changeset
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1 <tool id="diffbind" name="DiffBind" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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2 <description> differential binding analysis of ChIP-Seq peak data</description> |
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2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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diff
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3 <macros> |
18
f907216064f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
17
diff
changeset
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4 <token name="@TOOL_VERSION@">3.12.0</token> |
f907216064f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
17
diff
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5 <token name="@VERSION_SUFFIX@">0</token> |
17
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
16
diff
changeset
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6 <token name="@PROFILE@">22.05</token> |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
16
diff
changeset
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7 </macros> |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
16
diff
changeset
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8 <xrefs> |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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9 <xref type="bio.tools">diffbind</xref> |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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diff
changeset
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10 <xref type="bioconductor">diffbind</xref> |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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diff
changeset
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11 </xrefs> |
9
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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12 <requirements> |
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2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-diffbind</requirement> |
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f907216064f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
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changeset
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14 <requirement type="package" version="1.20.4">r-getopt</requirement> |
f907216064f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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15 <requirement type="package" version="4.0.16">bioconductor-edger</requirement> |
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6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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16 </requirements> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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17 <stdio> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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18 <regex match="Execution halted" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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19 source="both" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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20 level="fatal" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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21 description="Execution halted." /> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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22 <regex match="Input-Error 01" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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23 source="both" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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24 level="fatal" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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25 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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26 <regex match="Error in" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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27 source="both" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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28 level="fatal" |
12
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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29 description="An undefined error occured, please check your input carefully and contact your administrator." /> |
9
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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30 </stdio> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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31 <version_command><![CDATA[ |
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4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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32 echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
9
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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changeset
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33 ]]></version_command> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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34 <command><![CDATA[ |
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4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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35 #import re |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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36 #import json |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
10
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37 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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38 ## Adapted from DESeq2 wrapper |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
10
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changeset
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39 #set $temp_factor_names = list() |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
10
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changeset
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40 #set $temp_factor = list() |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
10
diff
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41 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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42 #for $g in $rep_group: |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
10
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43 |
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2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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44 #set $peak_files = dict() |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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diff
changeset
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45 #set $bam_files = dict() |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
16
diff
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46 #set $bam_controls = dict() |
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4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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47 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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48 #for $file in $g.peaks: |
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c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
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49 #set $file_name = str($g.groupName) + "-" + re.sub('[^\w\-]', '_', str($file.element_identifier)) + "-peaks.bed" |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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50 ln -s '${file}' '${file_name}' && |
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2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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51 #set $peak_files[str($file.element_identifier)] = str($file_name) |
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4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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52 #end for |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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53 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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54 #for $bam in $g.bamreads: |
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c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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55 #set $bam_name = re.sub('[^\w\-]', '_', str($bam.element_identifier)) |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
13
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56 #set $bam_file = $bam_name + "-bamreads.bam" |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
13
diff
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57 #set $bam_index = $bam_name + "-bamreads.bai" |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
13
diff
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58 ln -s '${bam}' '${bam_file}' && |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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59 ln -s '${bam.metadata.bam_index}' '${bam_index}' && |
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2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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60 #set $bam_files[str($bam.element_identifier)] = str($bam_file) |
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4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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61 #end for |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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62 |
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2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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63 #if len($peak_files.keys()) != len($bam_files.keys()) |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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64 >&2 echo "Group $g.groupName: same number of Peak and Bam files needs to be given" && exit 1 && |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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65 #end if |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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66 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($peak_files.items())]} ) |
2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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67 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($bam_files.items())]} ) |
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4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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68 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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69 #if str( $g.bamcontrol ) != 'None': |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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70 #for $ctrl in $g.bamcontrol: |
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c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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71 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier)) |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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72 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam" |
18
f907216064f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
parents:
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73 #set $ctrl_index = $ctrl_name + "-bamcontrol.bai" |
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c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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74 #if $ctrl_file not in json.dumps($temp_factor): |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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75 ln -s '${ctrl}' '${ctrl_file}' && |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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76 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' && |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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77 #end if |
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2605cbdaa7d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
iuc
parents:
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78 #set $bam_controls[str($ctrl.element_identifier)] = str($ctrl_file) |
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79 #end for |
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80 #if len($peak_files.keys()) != len($bam_files.keys()) |
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81 >&2 echo "Group $g.groupName: same number of Peak and Bam control files needs to be given" && exit 1 && |
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82 #end if |
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83 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($bam_controls.items())]} ) |
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84 #end if |
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85 |
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86 #end for |
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87 |
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88 $temp_factor.reverse() |
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89 $temp_factor_names.append(["Condition", $temp_factor]) |
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90 |
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91 |
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92 Rscript '$__tool_directory__/diffbind.R' |
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93 |
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94 -i '#echo json.dumps(temp_factor_names)#' |
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95 -o '$outfile' |
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96 -m '$method' |
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97 -t $th |
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98 -f $out.format |
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99 -p '$plots' |
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100 -O $minoverlap |
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101 #if $use_blacklist: |
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102 -B |
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103 #end if |
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104 -n $scorecol |
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105 #if $lowerbetter: |
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106 -l "$lowerbetter" |
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107 #end if |
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108 #if $summits: |
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109 -s "$summits" |
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110 #end if |
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111 |
11
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112 #if $out.binding_matrix: |
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113 -b |
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114 #end if |
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115 |
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116 #if $out.rdata: |
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117 -r |
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118 #end if |
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119 |
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120 #if $out.analysis_info: |
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121 -a |
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122 #end if |
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123 |
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124 #if $out.rscript: |
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125 && cp '$__tool_directory__/diffbind.R' '$rscript' |
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126 #end if |
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127 ]]> |
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128 </command> |
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129 <inputs> |
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130 <repeat name="rep_group" title="Group" min="2" max="2" default="2"> |
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131 <param name="groupName" type="text" label="Name" |
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132 help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores."> |
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133 <sanitizer> |
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134 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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135 </sanitizer> |
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136 <validator type="empty_field" /> |
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137 </param> |
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138 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/> |
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139 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM files" help="Specify the Read BAM files used in the Peak calling. The input order of the BAM files for the samples MUST match the input order of the peaks files."/> |
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140 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM files" help="If specifying a control BAM file, all samples are required to specify one, see Help section below. The input order of the BAM files for the samples MUST match the input order of the peaks files."/> |
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141 </repeat> |
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142 <param name="method" type="select" label="Underlying method by which to analyze differential binding affinity"> |
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143 <option value="DBA_DESEQ2" selected="True">DESeq2</option> |
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144 <option value="DBA_EDGER">edgeR</option> |
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145 </param> |
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146 <param name="use_blacklist" type="boolean" truevalue="True" falsevalue="" checked="False" label="Filters peak intervals that overlap a blacklist from ENCODE" help="Works with human, mouse, worm and fly. Assembly version is determined from the BAM files." /> |
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147 <param name="minoverlap" type="integer" min="1" value="2" label="Only include peaks in at least this many peaksets in the main binding matrix"> |
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148 <sanitizer> |
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149 <valid initial="string.digits"/> |
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150 </sanitizer> |
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151 </param> |
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152 <param name="scorecol" type="integer" min="0" value="5" label="Score Column" help="Column in peak files that contains peak scores. Default: 5 (narrowPeak)"> |
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153 <sanitizer> |
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154 <valid initial="string.digits"/> |
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155 </sanitizer> |
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156 </param> |
11
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157 <param name="lowerbetter" type="boolean" truevalue="True" falsevalue="" checked="False" label="Lower score is better?" help="DiffBind by default assumes that a higher score indicates a better peak, for example narrowPeaks -log10pvalue. If this is not the case, for example if the score is a p-value or FDR, set this option to Yes. Default: No" /> |
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158 <param name="summits" type="integer" min="0" optional="True" label="Summits" help="Extend peaks Nbp up- and downstream of the summit. For punctate peaks it is advisable to extend (e.g. 250bp), see the DiffBind User Guide"> |
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159 <sanitizer> |
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160 <valid initial="string.digits"/> |
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161 </sanitizer> |
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162 </param> |
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163 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/> |
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164 |
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165 <!-- Output Options --> |
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166 <section name="out" expanded="false" title="Output Options"> |
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167 <param name="format" type="select" label="Output Format"> |
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168 <option value="interval" selected="True">Interval</option> |
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169 <option value="bed">BED</option> |
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170 <option value="tabular">Tabular (tab-separated)</option> |
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171 </param> |
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172 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" /> |
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173 <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" /> |
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174 <param name="rdata" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. Default: No"/> |
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175 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/> |
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176 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/> |
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177 </section> |
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178 </inputs> |
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179 |
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180 <outputs> |
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181 <data name="outfile" format="interval" label="${tool.name} on ${on_string}: Differentially bound sites"> |
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182 <change_format> |
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183 <when input="out.format" value="bed" format="bed" /> |
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184 <when input="out.format" value="tabular" format="tabular" /> |
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185 </change_format> |
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186 </data> |
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187 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots"> |
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188 <filter>out['pdf']</filter> |
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189 </data> |
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190 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix"> |
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191 <filter>out['binding_matrix']</filter> |
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192 </data> |
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193 <data name="rdata" format="rdata" from_work_dir="DiffBind_analysis.RData" label="${tool.name} on ${on_string}: RData file"> |
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194 <filter>out['rdata']</filter> |
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195 </data> |
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196 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript"> |
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197 <filter>out['rscript']</filter> |
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198 </data> |
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199 <data name="analysis_info" format="txt" from_work_dir="DiffBind_analysis_info.txt" label="${tool.name} on ${on_string}: Analysis info"> |
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200 <filter>out['analysis_info']</filter> |
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201 </data> |
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202 </outputs> |
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203 |
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204 <tests> |
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205 <!-- Ensure outputs work --> |
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206 <test expect_num_outputs="6"> |
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207 <repeat name="rep_group"> |
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208 <param name="groupName" value="Resistant"/> |
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209 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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210 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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211 </repeat> |
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212 <repeat name="rep_group"> |
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213 <param name="groupName" value="Responsive"/> |
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214 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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215 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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216 </repeat> |
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217 <param name="scorecol" value="5" /> |
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218 <param name="format" value="interval"/> |
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219 <param name="pdf" value="True" /> |
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220 <param name="binding_matrix" value="True" /> |
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221 <param name="rdata" value="True" /> |
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222 <param name="rscript" value="True"/> |
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223 <param name="analysis_info" value="True"/> |
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224 <output name="outfile" ftype="interval" value="out_diffbind.interval" /> |
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225 <output name="plots" value="out_plots.pdf" compare="sim_size" /> |
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226 <output name="binding_matrix" value="out_binding_matrix.tab" /> |
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227 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/> |
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228 <output name="rscript"> |
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229 <assert_contents> |
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230 <has_text text="write.table"/> |
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231 </assert_contents> |
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232 </output> |
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233 <output name="analysis_info" compare="sim_size" > |
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234 <assert_contents> |
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235 <has_text text="SessionInfo"/> |
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236 </assert_contents> |
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237 </output> |
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238 </test> |
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239 <!-- Ensure EDGER works --> |
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240 <test expect_num_outputs="3"> |
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241 <repeat name="rep_group"> |
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242 <param name="groupName" value="Resistant"/> |
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243 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
f907216064f6
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244 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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245 </repeat> |
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246 <repeat name="rep_group"> |
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247 <param name="groupName" value="Responsive"/> |
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248 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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249 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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250 </repeat> |
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251 <param name="scorecol" value="5" /> |
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252 <param name="method" value="DBA_EDGER" /> |
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253 <param name="format" value="interval"/> |
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254 <param name="pdf" value="True" /> |
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255 <param name="binding_matrix" value="True" /> |
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256 <param name="rscript" value="False"/> |
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257 <output name="outfile" ftype="interval" value="out_diffbind_edger.interval" /> |
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258 <output name="plots" value="out_plots_edger.pdf" compare="sim_size" /> |
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259 <output name="binding_matrix" value="out_binding_matrix_edger.tab" /> |
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260 </test> |
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261 <!-- Ensure control BAMs input works --> |
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262 <test expect_num_outputs="1"> |
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263 <repeat name="rep_group"> |
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264 <param name="groupName" value="Resistant"/> |
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265 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
c97a786e8fb5
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266 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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267 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" /> |
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268 </repeat> |
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269 <repeat name="rep_group"> |
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270 <param name="groupName" value="Responsive"/> |
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271 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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272 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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273 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" /> |
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274 </repeat> |
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275 <param name="scorecol" value="5" /> |
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276 <param name="format" value="interval"/> |
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277 <output name="outfile" ftype="interval" value="out_diffbind_ctrl.interval" /> |
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278 </test> |
13
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279 <!-- Ensure BED output works --> |
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280 <test expect_num_outputs="1"> |
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281 <repeat name="rep_group"> |
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282 <param name="groupName" value="Resistant"/> |
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283 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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284 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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285 </repeat> |
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286 <repeat name="rep_group"> |
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287 <param name="groupName" value="Responsive"/> |
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288 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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289 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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290 </repeat> |
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291 <param name="scorecol" value="5" /> |
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292 <param name="format" value="bed"/> |
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293 <output name="outfile" ftype="bed" value="out_diffbind.bed" /> |
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294 </test> |
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295 <!-- Ensure tabular output works --> |
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296 <test expect_num_outputs="1"> |
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297 <repeat name="rep_group"> |
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298 <param name="groupName" value="Resistant"/> |
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299 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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300 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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301 </repeat> |
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302 <repeat name="rep_group"> |
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303 <param name="groupName" value="Responsive"/> |
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304 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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305 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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306 </repeat> |
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307 <param name="scorecol" value="5" /> |
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308 <param name="format" value="tabular"/> |
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309 <output name="outfile" ftype="tabular" file="out_diffbind.tab" /> |
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310 </test> |
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311 <!-- Ensure minoverlap works --> |
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312 <test expect_num_outputs="1"> |
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313 <repeat name="rep_group"> |
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314 <param name="groupName" value="Resistant"/> |
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315 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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316 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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317 </repeat> |
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318 <repeat name="rep_group"> |
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319 <param name="groupName" value="Responsive"/> |
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320 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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321 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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322 </repeat> |
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323 <param name="minoverlap" value="1" /> |
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324 <param name="scorecol" value="5" /> |
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325 <param name="format" value="tabular"/> |
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326 <output name="outfile" ftype="tabular" file="out_diffbind_minoverlap1.tab" /> |
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327 </test> |
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328 <!-- Ensure blacklist filtering works --> |
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329 <test expect_num_outputs="1"> |
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330 <repeat name="rep_group"> |
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331 <param name="groupName" value="Resistant"/> |
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332 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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333 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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334 </repeat> |
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335 <repeat name="rep_group"> |
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336 <param name="groupName" value="Responsive"/> |
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337 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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338 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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339 </repeat> |
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340 <param name="use_blacklist" value="True"/> |
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341 <param name="scorecol" value="5" /> |
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342 <param name="format" value="tabular"/> |
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343 <output name="outfile" ftype="tabular" file="out_diffbind_blacklist.tab" /> |
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344 </test> |
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345 </tests> |
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346 <help><![CDATA[ |
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347 |
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348 .. class:: infomark |
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349 |
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350 **What it does** |
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351 |
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352 DiffBind_ is a `Bioconductor package`_ that provides functions for processing ChIP-Seq data enriched for genomic loci where specific |
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353 protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and |
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354 aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, |
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355 representing different ChIP experiments (antibodies, transcription factor and/or histone |
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356 marks, experimental conditions, replicates) as well as managing the results of multiple peak |
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357 callers. |
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358 |
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359 The primary emphasis of DiffBind is on identifying sites that are differentially bound |
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360 between two sample groups. It includes functions to support the processing of peak sets, |
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361 including overlapping and merging peak sets, counting sequencing reads overlapping intervals |
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362 in peak sets, and identifying statistically significantly differentially bound sites based on |
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363 evidence of binding affinity (measured by differences in read densities). To this end it uses |
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364 statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages |
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365 edgeR and DESeq2). Additionally, the package builds on Rgraphics routines to provide a |
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366 set of standardized plots to aid in binding analysis. |
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367 |
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368 The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of |
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369 examples: the first focusing on the core task of obtaining differentially bound sites based on |
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370 affinity data, the second working through the main plotting routines, the third discussing the |
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371 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail, |
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372 as well as comparing the results of an occupancy-based analysis with an affinity-based one. |
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373 Finally, certain technical aspects of the how these analyses are accomplished are detailed. |
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374 |
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375 **Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).** |
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376 |
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377 ----- |
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378 |
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379 **Inputs** |
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380 |
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381 DiffBind works primarily with peaksets, which are sets of genomic intervals representing |
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382 candidate protein binding sites. Each interval consists of a chromosome, a start and end |
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383 position, and usually a score of some type indicating confidence in, or strength of, the peak. |
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384 Associated with each peakset are metadata relating to the experiment from which the peakset |
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385 was derived. Additionally, files containing mapped sequencing reads (BAM files) need to |
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386 be associated with each peakset (one for the ChIP data, and optionally another representing |
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387 a control sample) |
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388 |
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389 Inputs for a group will be sorted by identifier before processing. For each group the corresponding |
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390 sets of peak and BAM files need to be provided. Ideally this is accomplished by providing the data in |
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391 collections. |
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392 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
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|
393 |
12
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394 **Groups** |
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395 |
12
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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396 You have to specify the name of the Group and the peak and BAM files for the two Groups you want to compare (e.g Resistant and Responsive) in the tool form above. |
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397 |
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398 Example: |
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399 |
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400 ============= ============= |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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401 **Sample** **Group** |
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402 ------------- ------------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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403 BT4741 Resistant |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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404 BT4742 Resistant |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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405 MCF71 Responsive |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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406 MCF72 Responsive |
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407 ============= ============= |
9
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408 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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409 |
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410 **Peak files** |
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411 |
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412 Result of your Peak calling experiment in bed format, one file for each sample is required. The peak caller, format and score column can be specified in the tool form above. The default settings expect narrowPeak bed format, which has the score in the 8th column (-log10pvalue), and can be output from MACS2. |
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413 |
12
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414 Example: |
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415 |
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416 ======= ======= ======= =============== ============== |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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417 1 2 3 4 **5 (Score)** |
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418 ======= ======= ======= =============== ============== |
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419 chr18 215562 216063 peak_16037 56.11 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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420 chr18 311530 312105 peak_16038 222.49 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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421 chr18 356656 357315 peak_16039 92.06 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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422 chr18 371110 372092 peak_16040 123.86 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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423 chr18 395116 396464 peak_16041 1545.39 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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424 chr18 399014 400382 peak_16042 1835.19 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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425 chr18 499134 500200 peak_16043 748.32 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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426 chr18 503518 504552 peak_16044 818.30 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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427 chr18 531672 532274 peak_16045 159.30 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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428 chr18 568326 569282 peak_16046 601.11 |
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429 ======= ======= ======= =============== ============== |
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430 |
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431 * BAM file which contains the mapped sequencing reads associated with each peakset, one file for each sample is required. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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432 * Optional: Control BAM file representing a control dataset. If used, has to be specified for all samples. Note that the DiffBind authors say control reads are best utilized prior to running DiffBind, at the peak calling stage (e.g. with MACS2) and in blacklists, see this `Bioconductor post`_. |
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433 |
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434 ----- |
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435 |
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436 **Outputs** |
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437 |
10
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438 This tool outputs |
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439 |
13
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440 * a table of differentially bound sites in Interval, BED or Tabular 0-based format |
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441 |
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442 Optionally, under **Output Options** you can choose to output |
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443 |
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444 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots) |
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445 * a binding affinity matrix |
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446 * the R script used by this tool |
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447 * an RData file of the R objects generated |
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448 * a text file with information on the analysis (number of Intervals, FriP scores, method used) |
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449 |
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450 **Differentially Bound Sites** |
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451 |
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452 The default output is Interval format, for information on Interval format see here_. Alternatively, you can choose to output BED or Tabular 0-based format as below. For an explanation of the 0-based and 1-based coordinate systems see this `Biostars post`_. |
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453 |
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454 Example - **Interval format**: |
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455 |
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456 ====== ====== ====== ======== ===== ====== =========================================== |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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457 Chrom Start End Name Score Strand **Comment** |
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458 ====== ====== ====== ======== ===== ====== =========================================== |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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459 chr18 394599 396513 DiffBind 0 \. 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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460 chr18 111566 112005 DiffBind 0 \. 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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461 chr18 346463 347342 DiffBind 0 \. 879|5|5.77|3.24|2.52|6.51e-06|0.00303 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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462 chr18 399013 400382 DiffBind 0 \. 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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463 chr18 371109 372102 DiffBind 0 \. 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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464 ====== ====== ====== ======== ===== ====== =========================================== |
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465 |
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466 Columns contain the following data: |
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467 |
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468 * **Chrom**: Chromosome name |
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469 * **Start**: Start position of site |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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470 * **End**: End position of site |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
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471 * **Score**: 0 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
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472 * **Name**: DiffBind |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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473 * **Strand**: Strand |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
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474 * **Comment**: The pipe ("|") separated values in this column correspond to: |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
|
475 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
|
476 * *width*: Length of site |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
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477 * *Conc*: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted) |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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478 * *Conc_Group1*: Mean concentration over the first group (e.g. Responsive) |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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479 * *Conc_Group2*: Mean concentration over second group (e.g. Resistant) |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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480 * *Fold*: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group. |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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481 * *p.value*: P-value confidence measure for identifying these sites as differentially bound |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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482 * *FDR*: a multiple testing corrected FDR p-value |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
|
483 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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484 Example - **BED format**: |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
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485 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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486 ===== ====== ====== ======== ===== ====== |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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487 Chrom Start End Name Score Strand |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
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changeset
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488 ===== ====== ====== ======== ===== ====== |
18
f907216064f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
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changeset
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489 chr18 394599 396513 DiffBind 0 \. |
f907216064f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
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490 chr18 111566 112005 DiffBind 0 \. |
f907216064f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
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changeset
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491 chr18 346463 347342 DiffBind 0 \. |
f907216064f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
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changeset
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492 chr18 399013 400382 DiffBind 0 \. |
f907216064f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
iuc
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493 chr18 371109 372102 DiffBind 0 \. |
13
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
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494 ===== ====== ====== ======== ===== ====== |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
|
495 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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496 Example - **Tabular format**: |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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497 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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498 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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499 Chrom Start End Name Score Strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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500 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
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501 chr18 394599 396513 DiffBind 0 \. 7.15 5.55 7.89 -2.35 7.06E-24 9.84E-21 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
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changeset
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502 chr18 111566 112005 DiffBind 0 \. 5.71 6.53 3.63 2.89 1.27E-08 8.88E-06 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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503 chr18 346463 347342 DiffBind 0 \. 5 5.77 3.24 2.52 6.51E-06 0.00303 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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changeset
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504 chr18 399013 400382 DiffBind 0 \. 7.62 7 8.05 -1.04 1.04E-05 0.00364 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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505 chr18 371109 372102 DiffBind 0 \. 4.63 3.07 5.36 -2.3 8.10E-05 0.0226 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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506 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== |
9
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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507 |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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508 |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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509 **Binding Affinity Matrix** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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510 |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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511 The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent |
13
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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512 differential analysis. Note that this output is a tabular 0-based format. |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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513 |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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514 Example: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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515 |
12
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
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516 ===== ====== ====== ========= ========= ========== ========== |
13
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
iuc
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changeset
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517 Chrom Start End MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2 |
12
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
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518 ===== ====== ====== ========= ========= ========== ========== |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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changeset
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519 chr18 111567 112005 137.6152 59.87837 29.41393 19.95945 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
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520 chr18 189223 189652 19.95945 12.60597 11.55547 23.11095 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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521 chr18 215232 216063 11.55547 15.75746 31.51493 72.48434 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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522 chr18 311530 312172 17.85846 11.55547 54.62588 43.07040 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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523 chr18 346464 347342 75.63583 40.96941 21.00995 16.80796 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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524 chr18 356560 357362 11.55547 14.70696 57.77737 53.57538 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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525 chr18 371110 372102 8.403982 9.454479 81.93882 82.98932 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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526 chr18 394600 396513 56.72687 43.07040 510.5419 438.0575 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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527 chr18 399014 400382 156.5241 117.6557 558.8648 496.8854 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents:
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528 chr18 498906 500200 767.9138 278.3819 196.4430 181.7361 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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529 ===== ====== ====== ========= ========= ========== ========== |
9
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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530 |
10
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
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531 ----- |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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532 |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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533 **More Information** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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534 |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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535 Generally, processing data with DiffBind involves five phases: |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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changeset
|
536 |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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537 #. Reading in peaksets |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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538 #. Occupancy analysis |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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539 #. Counting reads |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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changeset
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540 #. Differential binding affinity analysis |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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changeset
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541 #. Plotting and reporting |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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changeset
|
542 |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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changeset
|
543 |
10
d7725c5596ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents:
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544 **Reading in peaksets**: |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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changeset
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545 |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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changeset
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546 The first step is to read in a set of peaksets and associated |
10
d7725c5596ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
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547 metadata. Peaksets are derived either from ChIP-Seq peak callers, such as **MACS2**, or using some other criterion (e.g. genomic windows, or all the promoter regions |
d7725c5596ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents:
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548 in a genome). A single experiment can have more than |
9
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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changeset
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549 one associated peakset; e.g. if multiple peak callers are used for comparison purposes |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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550 each sample would have more than one line in the sample sheet. Once the peaksets |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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551 are read in, a merging function finds all overlapping peaks and derives a single set of |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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552 unique genomic intervals covering all the supplied peaks (a consensus peakset for the |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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553 experiment). |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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554 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
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555 **Occupancy analysis**: |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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556 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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557 Peaksets, especially those generated by peak callers, provide |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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558 an insight into the potential occupancy of the protein being ChIPed for at specific |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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559 genomic loci. After the peaksets have been loaded, it can be useful to perform some |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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560 exploratory plotting to determine how these occupancy maps agree with each other, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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561 e.g. between experimental replicates (re-doing the ChIP under the same conditions), |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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562 between different peak callers on the same experiment, and within groups of samples |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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563 representing a common experimental condition. DiffBind provides functions to enable |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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564 overlaps to be examined, as well as functions to determine how well similar samples |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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565 cluster together. Beyond quality control, the product of an occupancy analysis may be |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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566 a consensus peakset, representing an overall set of candidate binding sites to be used |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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567 in further analysis. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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568 |
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569 **Counting reads**: |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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570 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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571 Once a consensus peakset has been derived, DiffBind can use the |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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572 supplied sequence read files to count how many reads overlap each interval for each |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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573 unique sample. The peaks in the consensus peakset may be re-centered and trimmed |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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574 based on calculating their summits (point of greatest read overlap) in order to provide |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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575 more standardized peak intervals. The final result of counting is a binding affinity matrix |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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576 containing a (normalized) read count for each sample at every potential binding site. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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577 With this matrix, the samples can be re-clustered using affinity, rather than occupancy, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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578 data. The binding affinity matrix is used for QC plotting as well as for subsequent |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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579 differential analysis. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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580 |
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581 **Differential binding affinity analysis**: |
9
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582 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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583 The core functionality of DiffBind is the |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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changeset
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584 differential binding affinity analysis, which enables binding sites to be identified that |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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585 are statistically significantly differentially bound between sample groups. To accomplish |
6171163112de
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586 this, first a contrast (or contrasts) is established, dividing the samples into groups to |
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587 be compared. Next the core analysis routines are executed, by default using DESeq2. |
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588 This will assign a p-value and FDR to each candidate binding site indicating confidence |
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589 that they are differentially bound. |
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590 |
10
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591 **Plotting and reporting**: |
9
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592 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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593 Once one or more contrasts have been run, DiffBind provides |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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594 a number of functions for reporting and plotting the results. MA plots give an |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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595 overview of the results of the analysis, while correlation heatmaps and PCA plots show |
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596 how the groups cluster based on differentially bound sites. Boxplots show the distribution |
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597 of reads within differentially bound sites corresponding to whether they gain or |
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598 lose affinity between the two sample groups. A reporting mechanism enables differentially |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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599 bound sites to be extracted for further processing, such as annotation, motif, and |
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600 pathway analyses. |
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601 |
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602 ----- |
9
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603 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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604 **References** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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605 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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606 DiffBind Authors: Rory Stark, Gordon Brown (2011) |
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607 Wrapper authors: Bjoern Gruening, Pavankumar Videm |
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608 |
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609 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
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610 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
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611 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf |
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612 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/ |
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613 .. _here: https://galaxyproject.org/learn/datatypes/#interval |
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614 .. _`Biostars post`: https://www.biostars.org/p/84686/ |
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615 |
9
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616 ]]> |
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617 </help> |
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618 <citations> |
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619 <citation type="doi">doi:10.1038/nature10730</citation> |
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620 </citations> |
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621 </tool> |