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Andy Pohl edited this page Dec 7, 2013 · 3 revisions

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)

Examples

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.

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