Mercurial > repos > greg > gregs
comparison bam_to_bigwig/README.txt @ 0:bc71417f212c
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| author | g2cmnty@test-web1.g2.bx.psu.edu |
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| date | Fri, 17 Jun 2011 15:25:25 -0400 |
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| -1:000000000000 | 0:bc71417f212c |
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| 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 The latest version of the bam_to_wiggle.py script is available at: | |
| 8 | |
| 9 https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py | |
| 10 | |
| 11 Place the script in the same directory as the XML configuration file, or | |
| 12 provide a soft link to it. | |
| 13 | |
| 14 This requires: | |
| 15 | |
| 16 Python2, version 2.6 or better | |
| 17 pysam (http://code.google.com/p/pysam/) | |
| 18 wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/) |