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arefeen / TAPAS

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Samtools or deptools #8

Closed JamalEH closed 4 years ago

JamalEH commented 4 years ago

Hi,

I tried to follow your pipeline to get the read coverage using samtools, but did not work. I got the following error: unrecognized command 'coverage'

Could you plase specify the command and options used to get the read coverage of each bam file? Can I use bedtools genomecov instead? or samtools depth, in default options?

Thank you in advance! Kind regards, Jamal.

arefeen commented 4 years ago

Hi Jamal,

There is a "Useful Commands" section in the github page. Try to follow the commands to generate the coverage file from bam file. Use the coverage file to run the tool.

Thanks, Ashraful

JamalEH commented 4 years ago

Hi dear, Thank you for your reply!

Indeed, everything is well explained in the code page and the paper. Sorry for that.

Kind regards, Jamal.