Question

Subsampling bam file - error DiffBind

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sergio.espeso-gil • 0

@sergioespeso-gil-6997

Last seen 4.8 years ago

New York

Hi community!

I am subsampling input control data for DiffBind analysis to test something. I have merged first input files by using samtools merge and then later samtools view -s "percentage of subsampling"

When I am trying to run DiffBind, then I get this error:

'subsampled_input.bam' does not appear to be a BAM file (bad magic number)

Any ideas? I am browsing in internet. I guess is a problem of the bam file, not of DiffBind. But if you could give some hints I will highly appreciate it.

Thanks

Sergio

diffbind samtools • 1.7k views

ADD COMMENT • link updated 7.7 years ago by Gord Brown ▴ 670 • written 7.7 years ago by sergio.espeso-gil • 0

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Are you *just* using the "-s" option? "samtools view" by default produces SAM output, not BAM. If you haven't already, try "samtools view -b -s ..."

ADD REPLY • link 7.7 years ago Gord Brown ▴ 670

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Thanks!!! That´s was the error, now working fine!

I could not live without youuuuuuuu and Rory hahaha THANKS!!!

ADD REPLY • link 7.7 years ago sergio.espeso-gil • 0

score 0 · Answer 1 · 2017-04-18

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Gord Brown ▴ 670

@gord-brown-5664

Last seen 4.0 years ago

United Kingdom

Adding the answer here, just so there's an actual "answer" as opposed to a comment:

Use the "-b" option to samtools to create BAM as opposed to SAM output.

ADD COMMENT • link 7.7 years ago Gord Brown ▴ 670