|
7
|
1 Convert a BAM file into a BigWig coverage file. This can be used directly from
|
|
|
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
|
|
|
4 region. This allows you to view regions of arbitrarily large Wiggle file data
|
|
|
5 at UCSC while avoiding the upload costs.
|
|
|
6
|
|
|
7 History
|
|
|
8 -------
|
|
|
9
|
|
|
10 v0.2.0 add a sort step after genomeCoverageBed which is required in some
|
|
|
11 instances otherwise bedGraphToBigWig will complain. This version also uses
|
|
|
12 Galaxy's dependency mechanism, added some tests, and updated some formatting.
|
|
|
13 By Lance Parsons.
|
|
|
14
|
|
|
15 v0.1.1 passes the forgotten split argument and moves to using the new
|
|
|
16 sub-command enabled bedtools. Thanks to David Leader.
|
|
|
17
|
|
|
18 As of v0.1.0, the Galaxy tools uses a revised bam_to_bigwig.py script using
|
|
|
19 genomeCoverageBed and bedGraphToBigWig - this approach allows gaps/skpis to
|
|
|
20 be excluded from the coverage calculation, which is important for RNA-Seq.
|
|
|
21
|
|
|
22 Until v0.0.2, this Galaxy tool used the bam_to_wiggle.py script from
|
|
|
23 https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py
|
|
|
24 which internally used pysam (and thus samtools) and wigToBigWig from UCSC.
|
|
|
25
|
|
|
26 Requirements
|
|
|
27 ------------
|
|
|
28
|
|
|
29 If you are installing this tool manually, place the Python script in the
|
|
|
30 same directory as the XML configuration file, or provide a soft link to it.
|
|
|
31 Ensure the following command line tools are on the system path:
|
|
|
32
|
|
|
33 pysam - Python interface to samtools (http://code.google.com/p/pysam/)
|
|
|
34 genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/)
|
|
|
35 bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
|
|
|
36
|
|
|
37 Credits
|
|
|
38 -------
|
|
|
39
|
|
|
40 Original script by Brad Chapman, revisions from Peter Cock including the
|
|
|
41 switch to using genomeCoverageBed and bedGraphToBigWig based on the work
|
|
|
42 of Lance Parsons.
|
|
|
43
|
|
|
44 License
|
|
|
45 ------
|
|
|
46
|
|
|
47 The code is freely available under the MIT license:
|
|
|
48 http://www.opensource.org/licenses/mit-license.html
|
