Mercurial > repos > malex > bayesase
annotate sam_compare_w_feature.xml @ 0:e979cb57a5d5 draft default tip
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
author | malex |
---|---|
date | Thu, 14 Jan 2021 21:51:36 +0000 |
parents | |
children |
rev | line source |
---|---|
0
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
1 <tool id="sam_compare_w_feature" name="Compare SAM Files and Create ASE Counts Tables" version="21.1.13"> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
2 <description> containing read counts for each parental genome </description> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
3 <macros> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
4 <import>macros.xml</import> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
5 </macros> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
6 <expand macro="requirements"/> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
7 <command><![CDATA[ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
8 sam_compare_w_feature.py |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
9 --fastq=$fastq |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
10 --sama=$sama |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
11 --samb=$samb |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
12 --feature=$feature |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
13 --length=`awk '{if(NR%4==2 && length) {count++; bases += length}} END {print bases/count}' ${fastq} | awk '{printf "%.0f", $1}'` |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
14 $nofqids |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
15 --counts=$counts |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
16 --totals=$totals |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
17 ]]></command> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
18 <inputs> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
19 <param name="fastq" type="data" format="fastq" label="FASTQ File" help="Select the FASTQ file used to generate the 2 SAM files [REQUIRED]"/> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
20 <param name="sama" type="data" format="tabular" label="SAM file with G1 reference" help="Select SAM file aligned to updated genome1 containing feature ID in RNAME field [REQUIRED]"/> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
21 <param name="samb" type="data" format="tabular" label="SAM file with G2 reference" help="Select SAM file for aligned to updated genome2 containing feature ID in RNAME field [REQUIRED]"/> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
22 <param name="feature" type="data" format="tabular" label="Reformatted BED file" help="Select BED file containing features to assign reads to, with feature ID names in first column. Can be a .tsv or .bed [REQUIRED]"/> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
23 <param name="nofqids" type="boolean" checked="false" truevalue="--nofqids" falsevalue="" label="Check FASTQ IDs" help="Select to skip checking SAM QNAME against the fastq sequence IDs. Saves time if already known to be good."/> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
24 </inputs> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
25 <outputs> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
26 <data name="counts" format="tsv" label="SAM Compare with Feature on ${on_string}: Create ASE Counts Tables" default_identifier_source="sama"/> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
27 <data name="totals" format="tsv" label="SAM Compare with Feature on ${on_string}: Create ASE Totals Tables" default_identifier_source="sama"/> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
28 </outputs> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
29 <tests> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
30 <test> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
31 <param name="fastq" ftype="data" value="align_and_counts_test_data/W55_M_1_1.fastq"/> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
32 <param name="sama" ftype="data" value="align_and_counts_test_data/W1118_G1_create_new_SAM_file_with_features_BASE_test_data.sam"/> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
33 <param name="samb" ftype="data" value="align_and_counts_test_data/W55_G2_create_new_SAM_file_with_features_BASE_test_data.sam" /> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
34 <param name="feature" ftype="data" value="align_and_counts_test_data/reformat_BED_file_for_BASE.bed" /> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
35 <param name="nofqids" ftype="boolean" value="--nofqids" /> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
36 <output name="counts" file="align_and_counts_test_data/ASE_counts_table_BASE_test_data.tsv" /> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
37 <output name="totals" file="align_and_counts_test_data/ASE_totals_table_BASE_test_data.tsv" /> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
38 </test> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
39 </tests> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
40 <help><![CDATA[ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
41 **Tool Description** |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
42 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
43 This tool compares the read mapping across two SAM files generated by mapping a FASTQ file to 2 genotype specific references. |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
44 The tool creates an ASE Counts Table for each FASTQ file by comparing the SAM files with genic features (created by the Create new SAM file tool) that were aligned to both genotype specific references. |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
45 Reads in each SAM file are processed and compared to determine whether a given read maps better to one genome or equally well to both. |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
46 The results are also displayed in a read count summary table. |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
47 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
48 **Input** |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
49 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
50 **FASTQ file [REQUIRED]** |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
51 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
52 The tool requires the FASTQ file used to generate the 2 SAM files. The FASTQ file is used to determine the APN (average number of reads per nucleotide). |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
53 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
54 **SAM files [Required]** |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
55 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
56 The tool requires the two SAM files of uniquely mapping reads output by the *Create New SAM file* tool. |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
57 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
58 (1) SAM file containing uniquely mapping reads that overlap with features of interest for updated reference genome G1 (SAM A). |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
59 (2) SAM file containing uniquely mapping reads that overlap with features of interest for updated reference genome G2 (SAM B). |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
60 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
61 **4- column BED file [Required]** |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
62 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
63 A four column BED file containing genic features in the 1st column and chromosome name in the 4th column. |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
64 This input BED file can be created using the *Reformat BED file* tool. |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
65 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
66 Example input BED File:: |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
67 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
68 +---------------+-----------+------------+------------+ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
69 | name | start | end | chrom | |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
70 +===============+===========+============+============+ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
71 | featureA | 2345 | 2899 | 2R | |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
72 +---------------+-----------+------------+------------+ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
73 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
74 **Output** |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
75 The tools generates 2 output TSV files: |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
76 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
77 1. An ASE counts table containing the orientation that unique reads mapped to each feature listed in the input Feature/BED |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
78 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
79 Example of ASE Counts Table |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
80 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
81 +---------------+------------+------------------+----------------+----------------+--------------------------+-------------------------+-------------------------+--------------------------+--------------------+--------------------+ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
82 |Feature_ID | BOTH_EXACT |BOTH_INEXACT_EQUAL|SAM_A_ONLY_EXACT|SAM_B_ONLY_EXACT| SAM_A_EXACT_SAM_B_INEXACT|SAM_B_EXACT_SAM_A_INEXACT|SAM_A_ONLY_SINGLE_INEXACT|SAM_B_ONLY_SINGLE_INEXACT |SAM_A_INEXACT_BETTER|SAM_B_INEXACT_BETTER| |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
83 +===============+============+==================+================+================+==========================+=========================+=========================+==========================+====================+====================+ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
84 | l(1)G0196 | 4 |2 | 0 | 0 | 0 | 0 |0 | 0 | 1 | 1 | |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
85 +---------------+------------+------------------+----------------+----------------+--------------------------+-------------------------+-------------------------+--------------------------+--------------------+--------------------+ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
86 | CG8920 |0 | 1 | 0 | 0 | 0 | 0 | 0 |0 |0 |0 | |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
87 +---------------+------------+------------------+----------------+----------------+--------------------------+-------------------------+-------------------------+--------------------------+--------------------+--------------------+ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
88 |CG10932 | 0 | 1 | 0 | 0 | 0 | 0 |0 |0 |0 | 0 | |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
89 +---------------+------------+------------------+----------------+----------------+--------------------------+-------------------------+-------------------------+--------------------------+--------------------+--------------------+ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
90 |Mapmodulin | 2 |1 |0 |0 | 0 | 0 | 0 | 0 | 0 | 1 | |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
91 +---------------+------------+------------------+----------------+----------------+--------------------------+-------------------------+-------------------------+--------------------------+--------------------+--------------------+ |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
92 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
93 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
94 ASE Counts Table headers: |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
95 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
96 (1) BOTH_EXACT: Number of reads that mapped uniquely to both genomes, and it was an exact match |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
97 (2) BOTH_INEXACT_EQUAL: Number of reads that mapped equally to both genomes (ie did not preferentially to a certain parental genome), but it was an inexact match |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
98 (3) {SAM_A/B}_ONLY_EXACT: Reads that mapped preferentially to only one of the two genomes and it was an exact match |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
99 (4) SAM_A_EXACT_SAM_B_INEXACT: Reads that mapped exactly to genome 1 and inexactly to parental genome 2 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
100 (5) SAM_B_EXACT_SAM_A_INEXACT: Reads that mapped exactly to genome 2 and inexactly to genome 1 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
101 (6) {SAM_A/B}_ONLY_SINGLE_INEXACT: Reads that mapped preferentially to only onegenome, and it was in an inexact manner |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
102 (7) {SAM_A/B}_INEXACT_BETTER: Reads that mapped preferentially to their opposite parent, but the match is inexact |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
103 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
104 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
105 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
106 2. An ASE totals table containing a summary of the reads aligning to the the G1 and G2 references |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
107 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
108 Example of ASE Totals Table:: |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
109 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
110 Count totals: |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
111 1: a_single_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
112 2: a_single_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
113 3: a_multi_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
114 4: a_multi_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
115 5: b_single_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
116 6: b_single_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
117 7: b_multi_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
118 8: b_multi_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
119 9: both_single_exact_same 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
120 10: both_single_exact_diff 6 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
121 11: both_single_inexact_same 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
122 12: both_single_inexact_diff 8 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
123 13: both_inexact_diff_equal 5 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
124 14: both_inexact_diff_a_better 1 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
125 15: both_inexact_diff_b_better 2 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
126 16: both_multi_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
127 17: both_multi_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
128 18: a_single_exact_b_single_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
129 19: a_single_inexact_b_single_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
130 20: a_single_exact_b_multi_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
131 21: a_multi_exact_b_single_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
132 22: a_single_exact_b_multi_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
133 23: a_multi_inexact_b_single_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
134 24: a_single_inexact_b_multi_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
135 25: a_multi_exact_b_single_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
136 26: a_single_inexact_b_multi_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
137 27: a_multi_inexact_b_single_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
138 28: a_multi_exact_b_multi_inexact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
139 29: a_multi_inexact_b_multi_exact 0 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
140 30: total_count 14 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
141 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
142 |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
143 ]]></help> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
144 <citations> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
145 <citation type="bibtex">@ARTICLE{Miller20BASE, |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
146 author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre}, |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
147 title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)}, |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
148 journal = {????}, |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
149 year = {submitted for publication} |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
150 }</citation> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
151 </citations> |
e979cb57a5d5
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
malex
parents:
diff
changeset
|
152 </tool> |