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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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2 Galaxy for display at UCSC. The advantage over standard Wiggle format is that 2 Galaxy for display at UCSC. The advantage over standard Wiggle format is that
3 the data is stored in a compressed format and can be retrieved by genome 3 the data is stored in a compressed format and can be retrieved by genome
4 region. This allows you to view regions of arbitrarily large Wiggle file data 4 region. This allows you to view regions of arbitrarily large Wiggle file data
5 at UCSC while avoiding the upload costs. 5 at UCSC while avoiding the upload costs.
6 6
7 The latest version of the bam_to_wiggle.py script is available at: 7 History
8 -------
8 9
10 As of v0.1.0, the Galaxy tools uses a revised bam_to_bigwig.py script using
11 genomeCoverageBed and bedGraphToBigWig - this approach allows gaps/skpis to
12 be excluded from the coverage calculation, which is important for RNA-Seq.
13
14 Until v0.0.2, this Galaxy tool used the bam_to_wiggle.py script from
9 https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py 15 https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py
16 which internally used pysam (and thus samtools) and wigToBigWig from UCSC.
10 17
11 Place the script in the same directory as the XML configuration file, or 18 Requirements
12 provide a soft link to it. 19 ------------
13 20
14 This requires: 21 If you are installing this tool manually, place the Python script in the
22 same directory as the XML configuration file, or provide a soft link to it.
23 Ensure the following command line tools are on the system path:
15 24
16 Python2, version 2.6 or better 25 pysam - Python interface to samtools (http://code.google.com/p/pysam/)
17 pysam (http://code.google.com/p/pysam/) 26 genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/)
18 wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/) 27 bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
28
29 Credits
30 -------
31
32 Original script by Brad Chapman, revisions from Peter Cock including the
33 switch to using genomeCoverageBed and bedGraphToBigWig based on the work
34 of Lance Parsons.