Question: How to estimate depth of coverage for a windows size on genome?
1
gravatar for Chen
5.0 years ago by
Chen830
Chen830 wrote:

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

depth of coverage doc • 3.5k views
ADD COMMENTlink modified 5.0 years ago by Istvan Albert ♦♦ 80k • written 5.0 years ago by Chen830
1
gravatar for Istvan Albert
5.0 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Istvan Albert ♦♦ 80k
1

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

ADD REPLYlink written 5.0 years ago by Chen830
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