Splitting BAM file from paired end into forward and reverse strands?

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4.9 years ago

Susmita Mandal ▴ 110

Hi,

I have splitted BAM file from single end reads into forward and reverse strands using the following command

samtools view -b -F 16 *for forward strand
samtools view -b -f 16 *for reverse strand

As I understand the sum of these two should be equal to the main BAM file. So my questing is for paired end reads, will it be different or the same code will work for both single and paired end reads? Help me understand.

Thanks,

Susmita

RNA-Seq samtools ngs rna-seq VCF • 2.0k views

ADD COMMENT • link 4.9 years ago by Susmita Mandal ▴ 110

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That code will pay no attention to any of the flags having to do with paired reads. It also won't pay attention to whether or not the read mapped.

ADD REPLY • link 4.9 years ago by swbarnes2 14k

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Can you be little more elaborative? I did not get it.

ADD REPLY • link 4.9 years ago by Susmita Mandal ▴ 110

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