annotate readdepth2sequencingdepth.xml @ 4:ecfc9041bcc5

Deleted selected files
author arkarachai-fungtammasan
date Wed, 01 Apr 2015 14:05:54 -0400
parents 20ab85af9505
children b27006b0a953
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
1 <tool id="readdepth2seqdepth" name="Convert informative read depth to sequencing depth" version="1.0.0">
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
2 <description>for flank-based mapping of microsatellites</description>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
3 <command interpreter="python2.7">sequencingdepthconversion_G.py $repeatlength $flanksize $readlength $infodepth $probprediction > $output </command>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
4
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
5 <inputs>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
6 <param name="repeatlength" type="integer" value="10" label="Repeat length (bp)" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
7 <param name="flanksize" type="integer" value="20" label="Required flank bases on each side in mapping" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
8 <param name="readlength" type="integer" value="100" label="Read length (treat all read as single end read)" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
9 <param name="infodepth" type="integer" value="5" label="Required read depth" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
10 <param name="probprediction" type="float" value="0.9" label="Proportion of genome that need certain level of read depth" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
11 </inputs>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
12 <outputs>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
13 <data format="input" name="output" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
14
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
15 </outputs>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
16 <tests>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
17 <!-- Test data with valid values -->
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
18 <test>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
19 <param name="repeatlength" value="10"/>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
20 <param name="flanksize" value="20" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
21 <param name="readlength" value="100" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
22 <param name="infodepth" value="5" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
23 <param name="probprediction" value="0.9" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
24 <output name="output" file="readdepth2seqdepth.out"/>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
25 </test>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
26
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
27 </tests>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
28 <help>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
29
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
30
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
31 .. class:: infomark
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
32
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
33 **What it does**
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
34
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
35 This tool is used to convert informative read depth (specified by user) to sequencing depth when the microsatellites is mapped using TRFM pipeline.
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
36 The locus specific sequencing depth is the sequencing depth that will make a certain loci have certain read depth based on uniform mapped of read. It is calculated as: ::
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
37
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
38 yrequired = ( X * L ) / (L - (2F+r-1))
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
39
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
40 Where X = read depth, L = read length, F = the number of flanked bases required on each flanking regions, r = the expected repeat length of microsatellite of interest.
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
41
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
42 The genome wide sequencing depth is the sequencing depth that will make certain percentage of genome (e.g. 90 percent or 95 percent) to have certain locus specific sequencing depth. It's calculated using numerical guessing to find smallest lambda that: ::
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
43
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
44 0.90 (or other proportion specified by user) &lt; = P(Y=0) + P(Y=1) + …+ P(Y=yrequired-1)
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
45
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
46 P(Y=y) = (lambda^(y) * e ^(-lambda)) /y!
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
47
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
48 y = specific level of sequencing depth. Lambda = genome wide sequencing depth
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
49
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
50
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
51 **Citation**
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
52
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
53 When you use this tool, please cite **Arkarachai Fungtammasan and Guruprasad Ananda (2014).**
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
54
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
55
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
56 </help>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
57 </tool>