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annotate bam_to_bigwig/README.txt @ 1:2f3ae18f13ed

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author g2cmnty@test-web1.g2.bx.psu.edu
date Tue, 21 Jun 2011 09:44:13 -0400
parents bc71417f212c
children
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g2cmnty@test-web1.g2.bx.psu.edu
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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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6
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7 The latest version of the bam_to_wiggle.py script is available at:
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8
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9 https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py
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11 Place the script in the same directory as the XML configuration file, or
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12 provide a soft link to it.
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13
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14 This requires:
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15
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16 Python2, version 2.6 or better
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17 pysam (http://code.google.com/p/pysam/)
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18 wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)