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Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
author Brad Chapman <chapmanb@50mail.com>
date Wed, 05 Sep 2012 21:14:54 -0400
parents 0ff100a057ef
children 294e9dae5a9b
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1 Convert a BAM file into a BigWig coverage file. This can be used directly from
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2 Galaxy for display at UCSC. The advantage over standard Wiggle format is that
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3 the data is stored in a compressed format and can be retrieved by genome
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4 region. This allows you to view regions of arbitrarily large Wiggle file data
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5 at UCSC while avoiding the upload costs.
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e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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7 History
e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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8 -------
e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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10 As of v0.1.0, the Galaxy tools uses a revised bam_to_bigwig.py script using
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11 genomeCoverageBed and bedGraphToBigWig - this approach allows gaps/skpis to
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12 be excluded from the coverage calculation, which is important for RNA-Seq.
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14 Until v0.0.2, this Galaxy tool used the bam_to_wiggle.py script from
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15 https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py
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16 which internally used pysam (and thus samtools) and wigToBigWig from UCSC.
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e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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18 Requirements
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19 ------------
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21 If you are installing this tool manually, place the Python script in the
e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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22 same directory as the XML configuration file, or provide a soft link to it.
e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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23 Ensure the following command line tools are on the system path:
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e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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25 pysam - Python interface to samtools (http://code.google.com/p/pysam/)
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26 genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/)
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27 bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
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29 Credits
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30 -------
e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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32 Original script by Brad Chapman, revisions from Peter Cock including the
e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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33 switch to using genomeCoverageBed and bedGraphToBigWig based on the work
e2edfa478eb4 Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
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34 of Lance Parsons.