Question: How to remove a chr from a bam file?
1
gravatar for mbk0asis
5.4 years ago by
mbk0asis570
Korea, Republic Of
mbk0asis570 wrote:

Hi.

If you want to remove reads mapped on a certain chr, how would you do that?

I know 'samtools' can extract reads on a chr. Extraction of each chr and combining chr data I want would solve the problem, but I have multiple bam files to run it. 

So, if anyone of you know how to REMOVE a single chr (e.g. chr1 only), please tell me.

Thank you!

rna-seq samtools • 6.3k views
ADD COMMENTlink written 5.4 years ago by mbk0asis570
6
gravatar for Ashutosh Pandey
5.4 years ago by
Philadelphia
Ashutosh Pandey12k wrote:

See this post: Remove mitochondrial reads from BAM files

ADD COMMENTlink written 5.4 years ago by Ashutosh Pandey12k

Thanks! It's the answer I wanted.

ADD REPLYlink written 5.4 years ago by mbk0asis570

I've moved Ashutosh's comment to an answer. Please accept it.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by RamRS30k
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