Mercurial > repos > rlegendre > ribo_tools
changeset 12:ee3a3435ce43 draft
Uploaded
| author | rlegendre |
|---|---|
| date | Fri, 23 Jan 2015 03:31:37 -0500 |
| parents | 313b8f7d2a92 |
| children | 7c944fd9907e |
| files | 313b8f7d2a92 |
| diffstat | 1 files changed, 395 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/313b8f7d2a92 Fri Jan 23 03:31:37 2015 -0500 @@ -0,0 +1,395 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en-US"> +<head> +<link rel="icon" href="/repos/rlegendre/ribo_tools/static/hgicon.png" type="image/png" /> +<meta name="robots" content="index, nofollow" /> +<link rel="stylesheet" href="/repos/rlegendre/ribo_tools/static/style-paper.css" type="text/css" /> +<script type="text/javascript" src="/repos/rlegendre/ribo_tools/static/mercurial.js"></script> + +<title>ribo_tools: 313b8f7d2a92</title> +</head> +<body> +<div class="container"> +<div class="menu"> +<div class="logo"> +<a href="http://mercurial.selenic.com/"> +<img src="/repos/rlegendre/ribo_tools/static/hglogo.png" alt="mercurial" /></a> +</div> +<ul> + <li><a href="/repos/rlegendre/ribo_tools/shortlog/313b8f7d2a92">log</a></li> + <li><a 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href="/repos/rlegendre/ribo_tools">ribo_tools</a> </h2> +<h3>changeset 11:313b8f7d2a92 <span class="tag">tip</span> </h3> + +<form class="search" action="/repos/rlegendre/ribo_tools/log"> + +<p><input name="rev" id="search1" type="text" size="30" /></p> +<div id="hint">Find changesets by keywords (author, files, the commit message), revision +number or hash, or <a href="/repos/rlegendre/ribo_tools/help/revsets">revset expression</a>.</div> +</form> + +<div class="description">(none)</div> + +<table id="changesetEntry"> +<tr> + <th class="author">author</th> + <td class="author">rlegendre</td> +</tr> +<tr> + <th class="date">date</th> + <td class="date age">Thu, 22 Jan 2015 14:34:53 +0100</td></tr> +<tr> + <th class="author">parents</th> + <td class="author"><a href="/repos/rlegendre/ribo_tools/rev/707807fee542">707807fee542</a> </td> +</tr> +<tr> + <th class="author">children</th> + <td class="author"></td> +</tr> +<tr> + <th class="files">files</th> + <td class="files"><a href="/repos/rlegendre/ribo_tools/file/313b8f7d2a92/get_codon_frequency.xml">get_codon_frequency.xml</a> <a href="/repos/rlegendre/ribo_tools/file/313b8f7d2a92/kmer_analysis.xml">kmer_analysis.xml</a> <a href="/repos/rlegendre/ribo_tools/file/313b8f7d2a92/metagene_frameshift_analysis.xml">metagene_frameshift_analysis.xml</a> <a href="/repos/rlegendre/ribo_tools/file/313b8f7d2a92/metagene_readthrough.xml">metagene_readthrough.xml</a> </td> +</tr> +<tr> + <th class="diffstat">diffstat</th> + <td class="diffstat"> + 4 files changed, 56 insertions(+), 55 deletions(-) + + <a id="diffstatexpand" href="javascript:toggleDiffstat()"/>[<tt>+</tt>]</a> + <div id="diffstatdetails" style="display:none;"> + <a href="javascript:toggleDiffstat()"/>[<tt>-</tt>]</a> + <p> + <table class="stripes2"> <tr> + <td class="diffstat-file"><a href="#l1.1">get_codon_frequency.xml</a></td> + <td class="diffstat-total" align="right">28</td> + <td class="diffstat-graph"> + <span class="diffstat-add" style="width:30.9523809524%;"> </span> + <span class="diffstat-remove" style="width:35.7142857143%;"> </span> + </td> + </tr> + <tr> + <td class="diffstat-file"><a href="#l2.1">kmer_analysis.xml</a></td> + <td class="diffstat-total" align="right">8</td> + <td class="diffstat-graph"> + <span class="diffstat-add" style="width:9.52380952381%;"> </span> + <span class="diffstat-remove" style="width:9.52380952381%;"> </span> + </td> + </tr> + <tr> + <td class="diffstat-file"><a href="#l3.1">metagene_frameshift_analysis.xml</a></td> + <td class="diffstat-total" align="right">42</td> + <td class="diffstat-graph"> + <span class="diffstat-add" style="width:52.380952381%;"> </span> + <span class="diffstat-remove" style="width:47.619047619%;"> </span> + </td> + </tr> + <tr> + <td class="diffstat-file"><a href="#l4.1">metagene_readthrough.xml</a></td> + <td class="diffstat-total" align="right">33</td> + <td class="diffstat-graph"> + <span class="diffstat-add" style="width:40.4761904762%;"> </span> + <span class="diffstat-remove" style="width:38.0952380952%;"> </span> + </td> + </tr> +</table> + </div> + </td> +</tr> +</table> + +<div class="overflow"> +<div class="sourcefirst linewraptoggle">line wrap: <a class="linewraplink" href="javascript:toggleLinewrap()">on</a></div> +<div class="sourcefirst"> line diff</div> +<div class="stripes2 diffblocks"> +<div class="bottomline inc-lineno"><pre class="sourcelines wrap"> +<span id="l1.1" class="minusline">--- a/get_codon_frequency.xml Thu Jan 22 14:34:38 2015 +0100</span><a href="#l1.1"></a> +<span id="l1.2" class="plusline">+++ b/get_codon_frequency.xml Thu Jan 22 14:34:53 2015 +0100</span><a href="#l1.2"></a> +<span id="l1.3" class="atline">@@ -1,5 +1,5 @@</span><a href="#l1.3"></a> +<span id="l1.4"> <tool id="Codon_analysis" name="Codon_density"></span><a href="#l1.4"></a> +<span id="l1.5" class="minusline">- <description> Analyse Ribo-seq alignments between two conditions to extract codon occupancy </description></span><a href="#l1.5"></a> +<span id="l1.6" class="plusline">+ <description>To compare Ribo-seq alignments between two sets of conditions, to determine codon occupancy </description></span><a href="#l1.6"></a> +<span id="l1.7"> <requirements></span><a href="#l1.7"></a> +<span id="l1.8"> <requirement type="package">samtools</requirement></span><a href="#l1.8"></a> +<span id="l1.9"> <requirement type="python-module">matplotlib</requirement></span><a href="#l1.9"></a> +<span id="l1.10" class="atline">@@ -32,7 +32,7 @@</span><a href="#l1.10"></a> +<span id="l1.11"> </command></span><a href="#l1.11"></a> +<span id="l1.12"> </span><a href="#l1.12"></a> +<span id="l1.13"> <inputs></span><a href="#l1.13"></a> +<span id="l1.14" class="minusline">- <param name="annot" type="data" label="References Input Annotation File (gff)" format="gff" /></span><a href="#l1.14"></a> +<span id="l1.15" class="plusline">+ <param name="annot" type="data" label="Reference annotation file (GFF)" format="gff" /></span><a href="#l1.15"></a> +<span id="l1.16"> <conditional name="replicat_opt"></span><a href="#l1.16"></a> +<span id="l1.17"> <param name="rep" type="select" label="Replicate option"></span><a href="#l1.17"></a> +<span id="l1.18"> <option value="yes">Yes (only two replicates by condition)</option></span><a href="#l1.18"></a> +<span id="l1.19" class="atline">@@ -40,23 +40,23 @@</span><a href="#l1.19"></a> +<span id="l1.20"> </param></span><a href="#l1.20"></a> +<span id="l1.21"> <when value="yes"></span><a href="#l1.21"></a> +<span id="l1.22"> ## Use conditional balise : if rep =yes : 4 files, else 2 files </span><a href="#l1.22"></a> +<span id="l1.23" class="minusline">- <param name="file1" type="data" label="First replicate of first condition (bam file)" format="bam" /></span><a href="#l1.23"></a> +<span id="l1.24" class="minusline">- <param name="file11" type="data" label="Second replicate of first condition (bam file)" format="bam" /></span><a href="#l1.24"></a> +<span id="l1.25" class="minusline">- <param name="file2" type="data" label="First replicate of second condition (bam file)" format="bam" /></span><a href="#l1.25"></a> +<span id="l1.26" class="minusline">- <param name="file22" type="data" label="First replicate of second condition (bam file)" format="bam" /></span><a href="#l1.26"></a> +<span id="l1.27" class="plusline">+ <param name="file1" type="data" label="First replicate of first condition (Bam file)" format="bam" /></span><a href="#l1.27"></a> +<span id="l1.28" class="plusline">+ <param name="file11" type="data" label="Second replicate of first condition (Bam file)" format="bam" /></span><a href="#l1.28"></a> +<span id="l1.29" class="plusline">+ <param name="file2" type="data" label="First replicate of second condition (Bam file)" format="bam" /></span><a href="#l1.29"></a> +<span id="l1.30" class="plusline">+ <param name="file22" type="data" label="First replicate of second condition (Bam file)" format="bam" /></span><a href="#l1.30"></a> +<span id="l1.31"> </when></span><a href="#l1.31"></a> +<span id="l1.32"> <when value="no"></span><a href="#l1.32"></a> +<span id="l1.33" class="minusline">- <param name="file1" type="data" label="First bam file" format="bam" /></span><a href="#l1.33"></a> +<span id="l1.34" class="minusline">- <param name="file2" type="data" label="Second bam File" format="bam" /></span><a href="#l1.34"></a> +<span id="l1.35" class="plusline">+ <param name="file1" type="data" label="First Bam file" format="bam" /></span><a href="#l1.35"></a> +<span id="l1.36" class="plusline">+ <param name="file2" type="data" label="Second Bam File" format="bam" /></span><a href="#l1.36"></a> +<span id="l1.37"> </when></span><a href="#l1.37"></a> +<span id="l1.38"> </conditional></span><a href="#l1.38"></a> +<span id="l1.39" class="minusline">- <param name="site" type="select" label="Please choose a ribosome site for codon analysis"></span><a href="#l1.39"></a> +<span id="l1.40" class="plusline">+ <param name="site" type="select" label="Please choose a ribosomal site for codon analysis"></span><a href="#l1.40"></a> +<span id="l1.41"> <option value="A">A</option></span><a href="#l1.41"></a> +<span id="l1.42"> <option value="P">P</option></span><a href="#l1.42"></a> +<span id="l1.43"> <option value="E">E</option></span><a href="#l1.43"></a> +<span id="l1.44"> </param></span><a href="#l1.44"></a> +<span id="l1.45"> <param name="asite" type="integer" label="Off-set from the 5'end of the footprint to the A-site" value ="15" /></span><a href="#l1.45"></a> +<span id="l1.46" class="minusline">- <param name="kmer" type="integer" label="Size of the best phasing reads" value ="28" /></span><a href="#l1.46"></a> +<span id="l1.47" class="plusline">+ <param name="kmer" type="integer" label="Lenght of the best phasing footprints" value ="28" /></span><a href="#l1.47"></a> +<span id="l1.48"> <param name="cond1" type="text" size="25" label="Condition one" help="Required even if no replicate" /></span><a href="#l1.48"></a> +<span id="l1.49"> <param name="cond2" type="text" size="25" label="Condition two" help="Required even if no replicate" /></span><a href="#l1.49"></a> +<span id="l1.50"> <param name="color1" type="text" size="50" label="Color for first condition" value ="SkyBlue" help="Enter standard name, hex color string, or rgb code. You cand find all colors here : http://pythonhosted.org/ete2/reference/reference_svgcolors.html" /></span><a href="#l1.50"></a> +<span id="l1.51" class="atline">@@ -74,14 +74,12 @@</span><a href="#l1.51"></a> +<span id="l1.52"> </span><a href="#l1.52"></a> +<span id="l1.53"> Summary</span><a href="#l1.53"></a> +<span id="l1.54"> ------- </span><a href="#l1.54"></a> +<span id="l1.55" class="minusline">-This tool uses Ribo-seq (bam file) to compare codon translation between two conditions.</span><a href="#l1.55"></a> +<span id="l1.56" class="minusline">-For each footprint, codons at choosen site are saved and an histogram with all normalized codon numbers is plotted in both conditions. </span><a href="#l1.56"></a> +<span id="l1.57" class="minusline">-A second histogram groups all codons corresponding to an amino acid.</span><a href="#l1.57"></a> +<span id="l1.58" class="minusline">-A chisquare test is used for testing if distribution of used codons is the same in both conditions.</span><a href="#l1.58"></a> +<span id="l1.59" class="plusline">+This tool uses Ribo-seq (BAM file) to determine whether codon occupancy differs between two sets of conditions. For each footprint, the codons at the chosen site are recorded and a histogram displaying all the normalised codon numbers is plotted for both sets of conditions. A second histogram groups together all the codons corresponding to a given amino acid. A chi-squared test is then carried out to determine whether the distribution of the codons used is the same in both sets of conditions.</span><a href="#l1.59"></a> +<span id="l1.60" class="plusline">+</span><a href="#l1.60"></a> +<span id="l1.61"> </span><a href="#l1.61"></a> +<span id="l1.62"> Output </span><a href="#l1.62"></a> +<span id="l1.63"> ------- </span><a href="#l1.63"></a> +<span id="l1.64" class="minusline">-This tool provides an html output with graphical outputs and a statistical test result. An additionnal csv file with codon numbers is provided. </span><a href="#l1.64"></a> +<span id="l1.65" class="plusline">+This tool provides an html file containing graphs and a statistical test result. An additional csv file with codon numbers is provided. </span><a href="#l1.65"></a> +<span id="l1.66"> </span><a href="#l1.66"></a> +<span id="l1.67"> </span><a href="#l1.67"></a> +<span id="l1.68"> Dependances</span><a href="#l1.68"></a></pre></div><div class="bottomline inc-lineno"><pre class="sourcelines wrap"> +<span id="l2.1" class="minusline">--- a/kmer_analysis.xml Thu Jan 22 14:34:38 2015 +0100</span><a href="#l2.1"></a> +<span id="l2.2" class="plusline">+++ b/kmer_analysis.xml Thu Jan 22 14:34:53 2015 +0100</span><a href="#l2.2"></a> +<span id="l2.3" class="atline">@@ -1,5 +1,5 @@</span><a href="#l2.3"></a> +<span id="l2.4"> <tool id="kmer_analysis" name="Kmer"></span><a href="#l2.4"></a> +<span id="l2.5" class="minusline">- <description>Compute proportion of each kmer and phasing</description></span><a href="#l2.5"></a> +<span id="l2.6" class="plusline">+ <description>To calculate the proportion and phasing of each kmer</description></span><a href="#l2.6"></a> +<span id="l2.7"> <requirements></span><a href="#l2.7"></a> +<span id="l2.8"> <requirement type="package">samtools</requirement></span><a href="#l2.8"></a> +<span id="l2.9"> <requirement type="package">numpy</requirement></span><a href="#l2.9"></a> +<span id="l2.10" class="atline">@@ -12,7 +12,7 @@</span><a href="#l2.10"></a> +<span id="l2.11"> </command></span><a href="#l2.11"></a> +<span id="l2.12"> </span><a href="#l2.12"></a> +<span id="l2.13"> <inputs></span><a href="#l2.13"></a> +<span id="l2.14" class="minusline">- <param name="gff" type="data" label="References Input Annotation File (gff)" format="gff" /></span><a href="#l2.14"></a> +<span id="l2.15" class="plusline">+ <param name="gff" type="data" label="Reference annotation file (GFF))" format="gff" /></span><a href="#l2.15"></a> +<span id="l2.16"> <param name="bamfile" type="data" label="Bam file" format="bam" /></span><a href="#l2.16"></a> +<span id="l2.17"> </inputs></span><a href="#l2.17"></a> +<span id="l2.18"> </span><a href="#l2.18"></a> +<span id="l2.19" class="atline">@@ -25,11 +25,11 @@</span><a href="#l2.19"></a> +<span id="l2.20"> </span><a href="#l2.20"></a> +<span id="l2.21"> Summary</span><a href="#l2.21"></a> +<span id="l2.22"> -------</span><a href="#l2.22"></a> +<span id="l2.23" class="minusline">-This tool uses Ribo-seq data (bam file) to compute proportion of each kmer (lenght of footprints) and phasing. </span><a href="#l2.23"></a> +<span id="l2.24" class="plusline">+The kmer tool computes the distribution of footprints length from Bam file and determines the proportion of footprints beginning in each frame, for all annotated genes in the GFF file.</span><a href="#l2.24"></a> +<span id="l2.25"> </span><a href="#l2.25"></a> +<span id="l2.26"> Output </span><a href="#l2.26"></a> +<span id="l2.27"> ------- </span><a href="#l2.27"></a> +<span id="l2.28" class="minusline">-This tool provides an html report with all kmer proportion and phasing. </span><a href="#l2.28"></a> +<span id="l2.29" class="plusline">+This tool provides an html report detailing the proportions and phasing of the kmers. </span><a href="#l2.29"></a> +<span id="l2.30"> </span><a href="#l2.30"></a> +<span id="l2.31"> </span><a href="#l2.31"></a> +<span id="l2.32"> Dependances</span><a href="#l2.32"></a></pre></div><div class="bottomline inc-lineno"><pre class="sourcelines wrap"> +<span id="l3.1" class="minusline">--- a/metagene_frameshift_analysis.xml Thu Jan 22 14:34:38 2015 +0100</span><a href="#l3.1"></a> +<span id="l3.2" class="plusline">+++ b/metagene_frameshift_analysis.xml Thu Jan 22 14:34:53 2015 +0100</span><a href="#l3.2"></a> +<span id="l3.3" class="atline">@@ -1,5 +1,5 @@</span><a href="#l3.3"></a> +<span id="l3.4"> <tool id="frameshift_analysis" name="Frame"></span><a href="#l3.4"></a> +<span id="l3.5" class="minusline">- <description> Analyse Ribo-seq alignment to extract translational ambiguities events</description></span><a href="#l3.5"></a> +<span id="l3.6" class="plusline">+ <description>To analyse Ribo-seq alignments for the extraction of translational ambiguities</description></span><a href="#l3.6"></a> +<span id="l3.7"> <requirements></span><a href="#l3.7"></a> +<span id="l3.8"> <requirement type="package">samtools</requirement></span><a href="#l3.8"></a> +<span id="l3.9"> <requirement type="python-module">matplotlib</requirement></span><a href="#l3.9"></a> +<span id="l3.10" class="atline">@@ -8,16 +8,18 @@</span><a href="#l3.10"></a> +<span id="l3.11"> <requirement type="python-module">Bio</requirement></span><a href="#l3.11"></a> +<span id="l3.12"> </requirements></span><a href="#l3.12"></a> +<span id="l3.13"> <command interpreter="python"> </span><a href="#l3.13"></a> +<span id="l3.14" class="minusline">- metagene_frameshift_analysis.py --input $reference --bam $mapping --cutoff $cutoff --kmer $kmer --fasta $fasta --dirout $output,$output.files_path --box $boxplot> $log</span><a href="#l3.14"></a> +<span id="l3.15" class="plusline">+ metagene_frameshift_analysis.py --gff $reference --bam $mapping --cutoff $cutoff --kmer $kmer --fasta $fasta --dirout $output,$output.files_path --box $boxplot --orf_length $orf --frame $frame > $log</span><a href="#l3.15"></a> +<span id="l3.16"> </span><a href="#l3.16"></a> +<span id="l3.17"> </command></span><a href="#l3.17"></a> +<span id="l3.18"> </span><a href="#l3.18"></a> +<span id="l3.19"> <inputs></span><a href="#l3.19"></a> +<span id="l3.20" class="minusline">- <param name="reference" type="data" label="References Input Annotation File (gff)" format="gff" /></span><a href="#l3.20"></a> +<span id="l3.21" class="minusline">- <param name="mapping" type="data" label="Bam Input File" format="bam" /></span><a href="#l3.21"></a> +<span id="l3.22" class="minusline">- <param name="fasta" type="data" label="Reference in fasta format" format="fasta" /></span><a href="#l3.22"></a> +<span id="l3.23" class="minusline">- <param name="kmer" type="integer" label="Longer of the best phasing reads" value ="28" /></span><a href="#l3.23"></a> +<span id="l3.24" class="plusline">+ <param name="reference" type="data" label="Reference annotation file (GFF)" format="gff" /></span><a href="#l3.24"></a> +<span id="l3.25" class="plusline">+ <param name="mapping" type="data" label="Bam file" format="bam" /></span><a href="#l3.25"></a> +<span id="l3.26" class="plusline">+ <param name="fasta" type="data" label="Reference genome in Fasta format" format="fasta" /></span><a href="#l3.26"></a> +<span id="l3.27" class="plusline">+ <param name="kmer" type="integer" label="Lenght of the best phasing footprints" value ="28" /></span><a href="#l3.27"></a> +<span id="l3.28" class="plusline">+ <param name="frame" type="integer" label="Frame where footprints show best phasing. Must be 1, 2 or 3" value ="1" /></span><a href="#l3.28"></a> +<span id="l3.29"> <param name="cutoff" type="integer" label="Cutoff for frame proportion in coding phase (default = 60 %)" value ="60" /></span><a href="#l3.29"></a> +<span id="l3.30" class="plusline">+ <param name="orf" type="integer" label="Approximate size of the segment (in bp)" value ="300" /> </span><a href="#l3.30"></a> +<span id="l3.31"> </inputs></span><a href="#l3.31"></a> +<span id="l3.32"> </span><a href="#l3.32"></a> +<span id="l3.33"> <outputs></span><a href="#l3.33"></a> +<span id="l3.34" class="atline">@@ -30,35 +32,35 @@</span><a href="#l3.34"></a> +<span id="l3.35"> <help></span><a href="#l3.35"></a> +<span id="l3.36"> Summary</span><a href="#l3.36"></a> +<span id="l3.37"> ------- </span><a href="#l3.37"></a> +<span id="l3.38" class="minusline">-This tool uses Ribo-seq data (bam file) to extract out-of-frame footprints in all genes from a reference annotation file (GFF3). Subprofile are plotted for each gene with dual coding events.</span><a href="#l3.38"></a> +<span id="l3.39" class="plusline">+This tool uses Ribo-seq data (BAM file) to extract out-of-frame footprints in all genes from a reference annotation file (GFF3). Subprofiles are plotted for each gene with dual coding events.</span><a href="#l3.39"></a> +<span id="l3.40"> </span><a href="#l3.40"></a> +<span id="l3.41"> </span><a href="#l3.41"></a> +<span id="l3.42" class="minusline">-*- GFF3 file* : It must contain 9 tabulate-delimited columns : Chromosome, source, feature, start, stop, score, strand, phasing, note. The gene ID was retrieved in note field by "ID=" tag.</span><a href="#l3.42"></a> +<span id="l3.43" class="plusline">+*- GFF3 file*: This file must have nine tabulated-delimited columns: Chromosome, source, feature, start, stop, score, strand, phasing, note. The gene ID is retrieved from the note field, using the "ID=" tag.</span><a href="#l3.43"></a> +<span id="l3.44"> </span><a href="#l3.44"></a> +<span id="l3.45" class="minusline">-*- Fasta file* : Reference fasta file. Be careful about the chromosome nomenclature used : it must be compatible with your GFF3 annotation file.</span><a href="#l3.45"></a> +<span id="l3.46" class="plusline">+*- Fasta file*: Reference fasta file. Care should be taken with the chromosome nomenclature used, which must be compatible with the GFF3 annotation file.</span><a href="#l3.46"></a> +<span id="l3.47"> </span><a href="#l3.47"></a> +<span id="l3.48" class="minusline">-*- BAM file* : It must be sorted. It can contain either multiples or unaligned footprints</span><a href="#l3.48"></a> +<span id="l3.49" class="plusline">+*- BAM file*: This file should be sorted and may contain either multiple or unaligned footprints</span><a href="#l3.49"></a> +<span id="l3.50"> </span><a href="#l3.50"></a> +<span id="l3.51" class="minusline">-*- Kmer* : Lenght of the best phasing footprint. You can compute it running kmer_analysis </span><a href="#l3.51"></a> +<span id="l3.52" class="plusline">+*- Kmer*: Length of the best-phased footprints. It can be calculated by running kmer_analysis </span><a href="#l3.52"></a> +<span id="l3.53" class="plusline">+</span><a href="#l3.53"></a> +<span id="l3.54" class="plusline">+*- Frame*: Frame for which the phasing of the footprints is best. It can be calculated by running kmer_analysis </span><a href="#l3.54"></a> +<span id="l3.55"> </span><a href="#l3.55"></a> +<span id="l3.56" class="minusline">-*- Cutoff* : Integer value for selecting all genes that have less than 60 % (default) of footprints in coding frame.</span><a href="#l3.56"></a> +<span id="l3.57" class="plusline">+*- Cutoff*: An integer value for selecting all genes for which fewer than 60 % (default) of the footprints are in the coding frame.</span><a href="#l3.57"></a> +<span id="l3.58"> </span><a href="#l3.58"></a> +<span id="l3.59" class="minusline">-</span><a href="#l3.59"></a> +<span id="l3.60" class="minusline">-</span><a href="#l3.60"></a> +<span id="l3.61" class="minusline">-.................................................................................................................................................................................................</span><a href="#l3.61"></a> +<span id="l3.62" class="plusline">+*- Orf*: Approximate size of the segment.</span><a href="#l3.62"></a> +<span id="l3.63"> </span><a href="#l3.63"></a> +<span id="l3.64"> </span><a href="#l3.64"></a> +<span id="l3.65"> </span><a href="#l3.65"></a> +<span id="l3.66"> Output </span><a href="#l3.66"></a> +<span id="l3.67"> ------- </span><a href="#l3.67"></a> +<span id="l3.68" class="minusline">-This tool generates 2 output files :</span><a href="#l3.68"></a> +<span id="l3.69" class="plusline">+This tool generates 3 output files:</span><a href="#l3.69"></a> +<span id="l3.70"> </span><a href="#l3.70"></a> +<span id="l3.71" class="minusline">-*- html file* : relative to translational ambiguities detection and visualization.</span><a href="#l3.71"></a> +<span id="l3.72" class="plusline">+*- html file*: for the detection and visualisation of translational ambiguities.</span><a href="#l3.72"></a> +<span id="l3.73"> </span><a href="#l3.73"></a> +<span id="l3.74" class="minusline">-*- Stat file* : statistiques about treated footprints and phasing.</span><a href="#l3.74"></a> +<span id="l3.75" class="plusline">+*- Stat file*: this file provides statistics for the treated footprints and phasing.</span><a href="#l3.75"></a> +<span id="l3.76"> </span><a href="#l3.76"></a> +<span id="l3.77" class="minusline">-*- Boxplot* : Proportion of footprints in the three frames for all genes.</span><a href="#l3.77"></a> +<span id="l3.78" class="minusline">-</span><a href="#l3.78"></a> +<span id="l3.79" class="plusline">+*- Boxplot*: Proportion of footprints in the three frames, for all genes.</span><a href="#l3.79"></a> +<span id="l3.80" class="plusline">+ </span><a href="#l3.80"></a> +<span id="l3.81"> </span><a href="#l3.81"></a> +<span id="l3.82"> Dependances</span><a href="#l3.82"></a> +<span id="l3.83"> ------------</span><a href="#l3.83"></a></pre></div><div class="bottomline inc-lineno"><pre class="sourcelines wrap"> +<span id="l4.1" class="minusline">--- a/metagene_readthrough.xml Thu Jan 22 14:34:38 2015 +0100</span><a href="#l4.1"></a> +<span id="l4.2" class="plusline">+++ b/metagene_readthrough.xml Thu Jan 22 14:34:53 2015 +0100</span><a href="#l4.2"></a> +<span id="l4.3" class="atline">@@ -1,5 +1,5 @@</span><a href="#l4.3"></a> +<span id="l4.4"> <tool id="readthrough_analysis" name="Stop_supp"></span><a href="#l4.4"></a> +<span id="l4.5" class="minusline">- <description> Analyse Ribo-seq alignment to detect readthrough events</description></span><a href="#l4.5"></a> +<span id="l4.6" class="plusline">+ <description>To analyse Ribo-seq alignments for the detection of stop codon readthrough events</description></span><a href="#l4.6"></a> +<span id="l4.7"> <requirements></span><a href="#l4.7"></a> +<span id="l4.8"> <requirement type="package">samtools</requirement></span><a href="#l4.8"></a> +<span id="l4.9"> <requirement type="python-module">HTseq</requirement></span><a href="#l4.9"></a> +<span id="l4.10" class="atline">@@ -8,14 +8,15 @@</span><a href="#l4.10"></a> +<span id="l4.11"> <requirement type="python-module">Bio</requirement></span><a href="#l4.11"></a> +<span id="l4.12"> </requirements></span><a href="#l4.12"></a> +<span id="l4.13"> <command interpreter="python"> </span><a href="#l4.13"></a> +<span id="l4.14" class="minusline">- metagene_readthrough.py --gff $gff --fasta $fasta --bam $mapping --dirout=$output,$output.files_path</span><a href="#l4.14"></a> +<span id="l4.15" class="plusline">+ metagene_readthrough.py --gff $gff --fasta $fasta --bam $mapping --dirout=$output,$output.files_path --extend $ext</span><a href="#l4.15"></a> +<span id="l4.16"> </span><a href="#l4.16"></a> +<span id="l4.17"> </command></span><a href="#l4.17"></a> +<span id="l4.18"> </span><a href="#l4.18"></a> +<span id="l4.19"> <inputs></span><a href="#l4.19"></a> +<span id="l4.20" class="minusline">- <param name="gff" type="data" label="References Input Annotation File (gff)" format="gff" /></span><a href="#l4.20"></a> +<span id="l4.21" class="minusline">- <param name="fasta" type="data" label="Reference in fasta format" format="fasta" /></span><a href="#l4.21"></a> +<span id="l4.22" class="minusline">- <param name="mapping" type="data" label="Bam Input File" format="bam" /></span><a href="#l4.22"></a> +<span id="l4.23" class="plusline">+ <param name="gff" type="data" label="Reference annotation file (GFF)" format="gff" /></span><a href="#l4.23"></a> +<span id="l4.24" class="plusline">+ <param name="fasta" type="data" label="Reference genome in Fasta format" format="fasta" /></span><a href="#l4.24"></a> +<span id="l4.25" class="plusline">+ <param name="mapping" type="data" label="Bam File" format="bam" /></span><a href="#l4.25"></a> +<span id="l4.26" class="plusline">+ <param name="ext" type="integer" label="Length of 3’ UTR extension downstream the annotated stop codon (in bp)" value="300" /></span><a href="#l4.26"></a> +<span id="l4.27"> </inputs></span><a href="#l4.27"></a> +<span id="l4.28"> </span><a href="#l4.28"></a> +<span id="l4.29"> <outputs></span><a href="#l4.29"></a> +<span id="l4.30" class="atline">@@ -25,28 +26,28 @@</span><a href="#l4.30"></a> +<span id="l4.31"> <help></span><a href="#l4.31"></a> +<span id="l4.32"> Summary</span><a href="#l4.32"></a> +<span id="l4.33"> ------- </span><a href="#l4.33"></a> +<span id="l4.34" class="minusline">-This tool uses Ribo-seq data (bam file) to extract potential genes with readthrough events from a reference annotation file (GFF3).</span><a href="#l4.34"></a> +<span id="l4.35" class="plusline">+This tool uses Ribo-seq data (BAM file) to extract genes displaying potential stop codon readthrough events from a reference annotation file (GFF3).</span><a href="#l4.35"></a> +<span id="l4.36"> </span><a href="#l4.36"></a> +<span id="l4.37" class="minusline">-C-terminal protein extensions were identified as previously described (Dunn J.G. and al, 2013). Only uniquely mapped footprints whose size is in the range 25 to 34 are considered.</span><a href="#l4.37"></a> +<span id="l4.38" class="minusline">-A gene is read-though if :</span><a href="#l4.38"></a> +<span id="l4.39" class="plusline">+C-terminal protein extensions were identified as previously described (Dunn J.G. et al, 2013). Only uniquely mapped footprints with a size in the 25 to 34 range are considered.</span><a href="#l4.39"></a> +<span id="l4.40" class="plusline">+A gene is considered to display readthrough if:</span><a href="#l4.40"></a> +<span id="l4.41"> </span><a href="#l4.41"></a> +<span id="l4.42"> i) It is covered by more than 128 footprints.</span><a href="#l4.42"></a> +<span id="l4.43"> </span><a href="#l4.43"></a> +<span id="l4.44" class="minusline">- ii) There are footprints after stop codon.</span><a href="#l4.44"></a> +<span id="l4.45" class="plusline">+ ii) There are footprints after the stop codon.</span><a href="#l4.45"></a> +<span id="l4.46"> </span><a href="#l4.46"></a> +<span id="l4.47" class="minusline">- iii) There are footprints overlapping the next in frame stop codon.</span><a href="#l4.47"></a> +<span id="l4.48" class="plusline">+ iii) There are footprints overlapping the next in-frame stop codon.</span><a href="#l4.48"></a> +<span id="l4.49"> </span><a href="#l4.49"></a> +<span id="l4.50" class="minusline">- iv) There is not Methionine in the next five codons downstream the official stop codon of CDS.</span><a href="#l4.50"></a> +<span id="l4.51" class="plusline">+ iv) There is no methionine codon in the next five codons downstream from the official stop codon of the CDS.</span><a href="#l4.51"></a> +<span id="l4.52"> </span><a href="#l4.52"></a> +<span id="l4.53" class="minusline">- v) The coverage is homogeneous within the extension.</span><a href="#l4.53"></a> +<span id="l4.54" class="plusline">+ v) Coverage is homogeneous within the extension.</span><a href="#l4.54"></a> +<span id="l4.55"> </span><a href="#l4.55"></a> +<span id="l4.56" class="minusline">-Stop codon readthrough was estimated by calculating a ratio between footprints in the C-terminal extension and in the CDS. Ribosome density footprints were estimated in RPKM (reads per kilobase per million). </span><a href="#l4.56"></a> +<span id="l4.57" class="minusline">-To control variability due to stop codon peaks, footprints mapping to stop codons are excluded to RPKM computing.</span><a href="#l4.57"></a> +<span id="l4.58" class="plusline">+Stop codon readthrough was estimated by calculating the ratio of the number of footprints in the C-terminal extension to that in the CDS. Ribosome density footprints were estimated in RPKM (reads per kilobase per million). We controlled for variability due to stop codon peaks, by excluding footprints mapping to stop codons from the calculation of RPKM.</span><a href="#l4.58"></a> +<span id="l4.59"> </span><a href="#l4.59"></a> +<span id="l4.60" class="plusline">+ </span><a href="#l4.60"></a> +<span id="l4.61"> Output </span><a href="#l4.61"></a> +<span id="l4.62"> ------- </span><a href="#l4.62"></a> +<span id="l4.63" class="minusline">-This tool produces html file with plots for each readthrough gene.</span><a href="#l4.63"></a> +<span id="l4.64" class="minusline">-</span><a href="#l4.64"></a> +<span id="l4.65" class="plusline">+This tool produces an html file with plots for each gene displaying readthrough.</span><a href="#l4.65"></a> +<span id="l4.66" class="plusline">+ </span><a href="#l4.66"></a> +<span id="l4.67"> </span><a href="#l4.67"></a> +<span id="l4.68"> Dependances</span><a href="#l4.68"></a> +<span id="l4.69"> ------------</span><a href="#l4.69"></a></pre></div> +</div> +</div> + +</div> +</div> +<script type="text/javascript">process_dates()</script> + + +</body> +</html> +