Mercurial > repos > lparsons > bam_to_bigwig
comparison README @ 3:b8525303b945
Reorganized repo
| author | Lance Parsons <lparsons@princeton.edu> |
|---|---|
| date | Wed, 24 Aug 2011 14:43:09 -0400 |
| parents | bam_to_bigwig/README@ed97c3e7e0bd |
| children |
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| 2:ed97c3e7e0bd | 3:b8525303b945 |
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| 1 Galaxy tool wrapper to generate BigWig coverage files from BAM files. BigWig | |
| 2 files can be displaye at UCSC directly from Galaxy. Allows user to split gapped | |
| 3 reads (particularly useful for RNA-Seq with large splice regions). | |
| 4 | |
| 5 Requirements | |
| 6 ------------ | |
| 7 genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/) | |
| 8 bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/) | |
| 9 | |
| 10 This tool also uses the samtools fai fasta index files stored in Galaxy's shared | |
| 11 tool data directory. A sample version of this file is included for completeness. | |
| 12 | |
| 13 Installation | |
| 14 ------------ | |
| 15 | |
| 16 1 - Install genomeCoverageBed and bedGraphToBigWig and make sure they in the PATH | |
| 17 2 - Copy bam_to_bigwig.xml to $GALAXY_HOME/tools/bam_to_bigwig | |
| 18 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file |