Question: 'BEDcov' and 'compute depth and breadth'
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gravatar for c.zijlstra
2.0 years ago by
c.zijlstra0
c.zijlstra0 wrote:

In galaxy I used boht the SAMtool bedcov and the bedtool 'Compute both depth and breath' to calculate the read depth in my samples. However, I get quite different numbers for depth with the two tools (depth in bedcov always higher), How can this be explained??

kind regards, carla

bedtools bed coverage samtools bam • 1.1k views
ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson25k • written 2.0 years ago by c.zijlstra0
0
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Samtools BedCov counts read that completely overlap the target intervals. BedTools Compute both depth and breath does a bit more - it counts partial overlaps, too.

The tool forms have more details and links to the manuals for the exact differences in the algorithms.

Best, Jen, Galaxy team

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Jennifer Hillman Jackson25k
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