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Hi everyone I would like to ask a question concerning, the use of FastP and gatk CollectSummaryAlignement.

I've used FastP for Preprocessing and I've specified the length requiered command to 30. After using the gatk CollectSummaryAlignment command to have an idea about my aligne reads, it shows that the minimum length is about 19 - 20 bp.

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raw quality_control preprocessing alignment reads
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written by AIMAR • AIMAR

1 answer

After using the gatk CollectSummaryAlignment command to have an idea about my aligne reads, it shows that the minimum length is about 19 - 20 bp.

That is probably reflective of the part of those 30+ bp reads that actually aligned to the reference you are using. Remainder of the read must be "soft-clipped" since those bases did not align (which you can confirm by checking CIGAR string for those alignments or visually via a genome viewer). If you check the length of the reads going into this alignment they should all be 30+bp.

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written by GenoMax GenoMax

How can I check the CIGAR string. And also do you have any idea about a genome browser I can use ?

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written by AIMAR • AIMAR

Understood and thanks

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written by AIMAR • AIMAR

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