Question

Soft Clipping Position

1

Entering edit mode

11.1 years ago

Nicolas Rosewick 11k

Hi,

How can I know the position and the length of soft-clipped nucleotides in my aligned reads (I used bowtie2 in local mode but the idea will be the same for other aligner). So from the sam file.

I put a little picture to explain more easily :

enter image description here

Thanks

N.

rna-seq • 4.3k views

ADD COMMENT • link updated 11.1 years ago by Zev.Kronenberg 12k • written 11.1 years ago by Nicolas Rosewick 11k

score 3 · Answer 1 · 2013-09-16

3

Entering edit mode

11.1 years ago

Zev.Kronenberg 12k

The answer you are looking for is in the SAM specification. The cigar string contains the information. Look for 'S' in the cigar string.

Nice picture.

ADD COMMENT • link 11.1 years ago by Zev.Kronenberg 12k

0

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I checked in SAM spec and indeed I have to filter by cigar flag. Thanks a lot

ADD REPLY • link 11.1 years ago by Nicolas Rosewick 11k