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Extract Only Paired-End Reads That Map A Specific Interval

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Hi,

Is it possible to extract paired-end reads that map to a specific interval ( from a bam file ). I tried with intersectBed :

intersectBed -abam align.bam -b interval.gff3 -wa > result.bam

here's the result :

enter image description here

But I only want reads that map to the feature in bold blue (one of the paired reads is enough). For example, I don't want the reads that map either side of this feature (red arrow).

Is it possible with intersectbed or an other program ?

Thanks,

N.


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