How to estimate depth of coverage for a windows size on genome?

Question

[Chen Sun]

Just as shown in following Figure a, for each point(small area?), I have a depth of coverage, and how can I get the red line, it seems that the red line is get from R package, and the value is average DOC of a consecutive area that DOC does not changes too much.

ref: Computational methods for discovering structural variation with next-generation sequencing

Paul Medvedev1, Monica Stanciu1 & Michael Brudno1,2

Answer 1

[Istvan Albert]

The answer is to use a tool that computes coverages. Please look on the right sidebar there are a number of good options.

Like: Coveragebed, Depth/Breadth Of Coverage

[Chen Sun]

Thanks Istvan, I think genomeCoverageBed perfectly solve my problem: http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html