Question: how to extract the sense and antisene bam files from the single end mapping bam file?
1
gravatar for wu.zhiqiang.1020
4.5 years ago by
United States
wu.zhiqiang.102020 wrote:

Dear  all,

I have one bam file produced from single end RNAseq reads using Gsnap. I want to extract the separated bam files for sense and antisense reads only.

I know that the samtools could use to extract them by flag for pair ens read bam file. But what's the flag number for single end reads bam file? what's the commands for single end bam file?

Or what other tools could be used to extract the sense and antisense reads bam file from one total bam file?

Thanks!

ZQ

rna-seq • 2.4k views
ADD COMMENTlink modified 4.5 years ago by Pierre Lindenbaum122k • written 4.5 years ago by wu.zhiqiang.102020
0
gravatar for Pierre Lindenbaum
4.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k wrote:

it's the same flag: use  -f 16 or -F 16  to include/exclude the reads on the reverse strand


 

ADD COMMENTlink written 4.5 years ago by Pierre Lindenbaum122k

If you want to split the file according to the strand, you should follow Pierre's answer.

If you want to have the sense/antisense reads according to the transcripts' orientation, you should use for instance intersectBed with the -s and -S options.

ADD REPLYlink written 4.5 years ago by michael.ante3.3k

Thanks. I will do your suggestion to try. if I have problem, I will post here. Cheers!

ADD REPLYlink written 4.5 years ago by wu.zhiqiang.102020
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