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Way to check if there is local trimmed alihned reads BOWTIE2

Is there a way to check if there is a trimmed/clipped reads aligned and how much are they from my attempt of running bowtie2 --local mode?

bowtie2
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updated by Ram Ram • written by manekineko manekineko

1 answer

You can read the CIGAR code in the SAM file. Look for H and S which represent hard clipping and soft clipping. The number in front of the H and S indicates the number of clipping.

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written by Sam Sam

Something like the following gives you the total number of soft- and hard-clipped reads

samtools view my.bam | cut -f6 | sed -n '/^[0-9]\+[SH]\|[0-9]\+[SH]$/p' | wc -l
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written by thackl thackl

Thanks, I want to check as my reads are quite short 20-25, and I used --local and seed -L 8, but in the IGV I do not see any clipped reads aligned near exon-intron sites? I'm running you command now .....

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written by manekineko manekineko

You might have to fiddle with your scoring parameters and filter for those short reads. See Bowtie2-manual --local and --score-min. Otherwise clipped reads might just not be reported.

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written by thackl thackl

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