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chromgraph
Andy Pohl edited this page Dec 7, 2013
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The chromgraph format is explained on the Genome Graphs User Guide page but in the case of bwtool we're only concerned with the bed-like chromgraph format. In this case it's just a chromosome, a coordinate, and a value. Because there's only one coordinate, bwtool will interpret this coordinate as the center of a range of values, and averages this.
The command-line message:
bwtool chromgraph - produce a chromgraph file usable by the UCSC Genome Graphs tool
usage:
bwtool chromgraph input.bw[:chr:start-end] output.txt
options:
-every=N Output datapoints every N bases instead of default (10,000 bp)
With the usual example:
and making a plot point every 5 bases will give:
$ bwtool chromgraph -every=5 main.bw stdout
chr 2 3.80
chr 7 4.20
chr 12 3.40
chr 17 4.60
chr 22 1.67
chr 27 3.00
chr 32 4.80
chr 35 2.00
This example is only to explain the inner-workings of the program. A more useful example can be found here.