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Question: Bedtools coverage not accepting file b
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gravatar for tran_tim
2.2 years ago by
tran_tim • 10
tran_tim • 10 wrote:

Bedtools coverage does not accept the -b files.

Compute both the depth and breadth of coverage of features in file A across the features in file B (coverageBed) . I can chose file A the bed files , but not file B which is my Bam files. What is wrong?

Tim
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modified 2.2 years ago by Bjoern Gruening ♦ 5.1k • written 2.2 years ago by tran_tim • 10

Hi Tim, I understand you are using the tool compute both depth and breadth of coverage. Can you explain to me whether the outtput of this tool represents number of nucleotides mapped to a region, or number of alignments?

Kind regards, carla

ADD REPLY • link written 2.1 years ago by c.zijlstra • 0
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gravatar for Bjoern Gruening
2.2 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

can you tell me which tool version you are using and on which server? Looking at the Galaxy tool source, it looks like this should work:

https://github.com/galaxyproject/tools-iuc/blob/master/tools/bedtools/coverageBed.xml

Sorry for the trouble, Bjoern
ADD COMMENT • link written 2.2 years ago by Bjoern Gruening ♦ 5.1k
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