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Soft Clipping Position

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
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updated by Zev.Kronenberg Zev.Kronenberg • written by Nicolas Rosewick Nicolas Rosewick

1 answer

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.

• 129 views • link
written by Zev.Kronenberg Zev.Kronenberg

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

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

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