Mercurial > repos > lparsons > bam_to_bigwig

view README @ 5:5b40b93ebae3 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added advanced settings
author Lance Parsons <lparsons@princeton.edu>
date Wed, 24 Aug 2011 16:44:28 -0400
parents b8525303b945
children
line wrap: on
line source

Galaxy tool wrapper to generate BigWig coverage files from BAM files. BigWig
files can be displaye at UCSC directly from Galaxy. Allows user to split gapped
reads (particularly useful for RNA-Seq with large splice regions).

Requirements
------------
genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/)
bedGraphToBigWig  - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)

This tool also uses the samtools fai fasta index files stored in Galaxy's shared
tool data directory. A sample version of this file is included for completeness. 

Installation
------------

1 - Install genomeCoverageBed and bedGraphToBigWig and make sure they in the PATH 
2 - Copy bam_to_bigwig.xml to $GALAXY_HOME/tools/bam_to_bigwig
3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file