Mercurial > repos > brad-chapman > bam_to_bigwig
view bam_to_bigwig/README.txt @ 4:14e5258d1b39
v0.1.1: Add the forgotten --split argument in XML and moves to using the new bedtools. Thanks to David Leader
author | Brad Chapman <chapmanb@50mail.com> |
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date | Tue, 11 Feb 2014 15:55:22 -0500 |
parents | 294e9dae5a9b |
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Convert a BAM file into a BigWig coverage file. This can be used directly from Galaxy for display at UCSC. The advantage over standard Wiggle format is that the data is stored in a compressed format and can be retrieved by genome region. This allows you to view regions of arbitrarily large Wiggle file data at UCSC while avoiding the upload costs. History ------- v0.1.1 passes the forgotten split argument and moves to using the new sub-command enabled bedtools. Thanks to David Leader. As of v0.1.0, the Galaxy tools uses a revised bam_to_bigwig.py script using genomeCoverageBed and bedGraphToBigWig - this approach allows gaps/skpis to be excluded from the coverage calculation, which is important for RNA-Seq. Until v0.0.2, this Galaxy tool used the bam_to_wiggle.py script from https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py which internally used pysam (and thus samtools) and wigToBigWig from UCSC. Requirements ------------ If you are installing this tool manually, place the Python script in the same directory as the XML configuration file, or provide a soft link to it. Ensure the following command line tools are on the system path: pysam - Python interface to samtools (http://code.google.com/p/pysam/) genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/) bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/) Credits ------- Original script by Brad Chapman, revisions from Peter Cock including the switch to using genomeCoverageBed and bedGraphToBigWig based on the work of Lance Parsons. License ------ The code is freely available under the MIT license: http://www.opensource.org/licenses/mit-license.html