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Question: 'BEDcov' and 'compute depth and breadth'
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gravatar for c.zijlstra
2.1 years ago by
c.zijlstra • 0
c.zijlstra • 0 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
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modified 2.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by c.zijlstra • 0
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gravatar for Jennifer Hillman Jackson
2.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 2.1 years ago • written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k
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