Question

Extract R1 Alignment Informations From Bam

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10.8 years ago

Nicolas Rosewick 11k

Hi,

Simple question : How to extract only aignment from R1 read from a bam file ?

Thanks

bam • 4.3k views

ADD COMMENT • link updated 10.8 years ago by Devon Ryan 104k • written 10.8 years ago by Nicolas Rosewick 11k

score 2 · Answer 1 · 2014-03-04

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10.8 years ago

Devon Ryan 104k

samtools view -f 0x40 alignments.bam

ADD COMMENT • link 10.8 years ago by Devon Ryan 104k

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great that's perfect !

ADD REPLY • link 10.8 years ago by Nicolas Rosewick 11k

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This gives first in pair reads. But what about the reads which are not in pair i.e., R1 has aligned but not R2. I see R1's with flag 0 and 16 also.

ADD REPLY • link 10.0 years ago by ashwini ▴ 100

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Then the aligner is setting the flags incorrectly. If a read came from a pair, then it should never have a flag of 0 or 16.

ADD REPLY • link 10.0 years ago by Devon Ryan 104k