Mercurial > repos > erasmus-medical-center > dr_disco
changeset 11:3743fd602fa9 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
| author | erasmus-medical-center |
|---|---|
| date | Fri, 03 Nov 2017 07:23:57 -0400 |
| parents | f2c70d589596 |
| children | |
| files | dr-disco_classify.xml dr-disco_detect.xml dr-disco_fix.xml dr-disco_integrate.xml |
| diffstat | 4 files changed, 22 insertions(+), 12 deletions(-) [+] |
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--- a/dr-disco_classify.xml Thu Nov 02 05:17:31 2017 -0400 +++ b/dr-disco_classify.xml Fri Nov 03 07:23:57 2017 -0400 @@ -110,13 +110,15 @@ **What it does** -It filters fusion events that are likely to be true or false based on a variety of parameters provided in the input table. +* Step 3 in dr-disco pipeline -**Attributions** +This tools filters the detected junctions which are likely to be true or false based on a variety of parameters provided in the input table. This filtering is in particular based on variables derived from the shape of the alignment and the ratio of split and spanning reads. + +**Attribution** This work is part of Youri Hoogstrate's PhD thesis. ]]></help> <expand macro="citations"/> -</tool> \ No newline at end of file +</tool>
--- a/dr-disco_detect.xml Thu Nov 02 05:17:31 2017 -0400 +++ b/dr-disco_detect.xml Fri Nov 03 07:23:57 2017 -0400 @@ -34,18 +34,17 @@ </tests> <help><![CDATA[ - **What it does** -Detects junctions in ('dr-disco fix' prepared) Chimeric alignments and tries to reconstruct fusion genes and genomic breakpoints using a Graph data structure. +* Step 2 in dr-disco pipeline -This software is in particular designed for RNA-Seq data prepared with random hexamer priming because of the presence of intronic reads. +This tool detects junctions in ('dr-disco fix' prepared) Chimeric alignments and tries to reconstruct fusion genes and genomic breakpoints using a Graph data structure. This software is in particular designed for RNA-Seq data prepared with random hexamer priming because of the presence of intronic reads. -**Attributions** +**Attribution** This work is part of Youri Hoogstrate's PhD thesis. ]]></help> <expand macro="citations"/> -</tool> \ No newline at end of file +</tool>
--- a/dr-disco_fix.xml Thu Nov 02 05:17:31 2017 -0400 +++ b/dr-disco_fix.xml Fri Nov 03 07:23:57 2017 -0400 @@ -33,8 +33,14 @@ **What it does** -Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (detect) and for visualization in genome browsers. +* Step 1 in dr-disco pipeline + +Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (detect) and for visualization in genome browsers by modifying certain SAM flags and tags. + +**Attribution** + +This work is part of Youri Hoogstrate's PhD thesis. ]]></help> <expand macro="citations"/> -</tool> \ No newline at end of file +</tool>
--- a/dr-disco_integrate.xml Thu Nov 02 05:17:31 2017 -0400 +++ b/dr-disco_integrate.xml Fri Nov 03 07:23:57 2017 -0400 @@ -48,12 +48,15 @@ **What it does** +* Step 4 in dr-disco pipeline -**Attributions** +In this step the predicted junctions are integrated with a gene annotation. The junctions are provided names like 'TMPRSS2->ERG' and frameshift are provided. Also events that belong to each other, thus the intronic and exonic junctions that belong to the same genomic event, are given the same identifier. + +**Attribution** This work is part of Youri Hoogstrate's PhD thesis. ]]></help> <expand macro="citations"/> -</tool> \ No newline at end of file +</tool>