intersectBed: -s option not working while intersecting a bam file

[Amit Anand]

Hi Aaron,


I have just started using Bedtools.
I am having problem while using -s option in following conditions,

intersectBed -abam a.bam -b b.bed -s -bed -wb


In essence I want to intersect this bam file to get an output with
enforced strandedness and with original features of b.bed, in bed
format.

Please help me with this.

Thank you,

Amit

[Aaron Quinlan]

Hi Amit,

Please try the version in the repository [1], as it works for me:

bedtools intersect -abam HG00739.chr20.possrt.bam -b simrep.bed -s -bed -wb | head
22 16059465 16059496 SRR069529.42985603/1 15 + 16059451 16059552 0,0,0 1 101, 0, 22 16059465 16059496 trf 53 +
22 16059485 16059496 SRR069529.103215282/2 0 + 16059485 16059586 0,0,0 1 101, 0, 22 16059465 16059496 trf 53 +
22 16060479 16060493 SRR069529.112563411/1 46 + 16060392 16060493 0,0,0 1 101, 0, 22 16060479 16060524 trf 90 +
22 16060479 16060493 SRR069529.112563411/1 46 + 16060392 16060493 0,0,0 1 101, 0, 22 16060479 16060592 trf 120 +
22 16060490 16060524 SRR069529.105005265/2 60 + 16060490 16060593 0,0,0 1 103, 0, 22 16060479 16060524 trf 90 +
22 16060490 16060592 SRR069529.105005265/2 60 + 16060490 16060593 0,0,0 1 103, 0, 22 16060479 16060592 trf 120 +
22 16060517 16060593 SRR069529.105005265/2 60 + 16060490 16060593 0,0,0 1 103, 0, 22 16060517 16060609 trf 129 +
22 16060491 16060524 SRR069529.8032613/1 37 + 16060491 16060571 0,0,0 1 80, 0, 22 16060479 16060524 trf 90 +
22 16060491 16060571 SRR069529.8032613/1 37 + 16060491 16060571 0,0,0 1 80, 0, 22 16060479 16060592 trf 120 +
22 16060517 16060571 SRR069529.8032613/1 37 + 16060491 16060571 0,0,0 1 80, 0, 22 16060517 16060609 trf 129 +

[1] https://github.com/arq5x/bedtools

Best,
Aaron