Subsampling bam file - error DiffBind
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@sergioespeso-gil-6997
Last seen 4.1 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 • 1.4k views
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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 ..."

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

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

 

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Gord Brown ▴ 650
@gord-brown-5664
Last seen 3.2 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.

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