Mercurial > repos > lparsons > bam_to_bigwig

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Added advanced settings
author Lance Parsons <lparsons@princeton.edu>
date Wed, 24 Aug 2011 16:44:28 -0400
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1 Galaxy tool wrapper to generate BigWig coverage files from BAM files. BigWig
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2 files can be displaye at UCSC directly from Galaxy. Allows user to split gapped
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3 reads (particularly useful for RNA-Seq with large splice regions).
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5 Requirements
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6 ------------
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7 genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/)
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8 bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
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10 This tool also uses the samtools fai fasta index files stored in Galaxy's shared
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11 tool data directory. A sample version of this file is included for completeness.
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13 Installation
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14 ------------
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16 1 - Install genomeCoverageBed and bedGraphToBigWig and make sure they in the PATH
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17 2 - Copy bam_to_bigwig.xml to $GALAXY_HOME/tools/bam_to_bigwig
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18 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file