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unique379r / strspy

STRspy: a novel alignment and quantification-based state-of-the-art method, short tandem repeat (STR) detection calling tool designed specifically for long-read sequencing reads such as from Oxford nanopore technology (ONT) and PacBio.
MIT License
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Primary alignment filtering #3

Open HJeffery opened 2 years ago

HJeffery commented 2 years ago

Hi,

I've found a way to reduce background repeat counts.

In line 333 of https://github.com/unique379r/strspy/blob/main/scripts/STRspy_v1.0.sh reads are filtered so that only unmapped are eliminated from repeat counting.

If swapped to keep only primary alignments (-F 2308) instead of -F 4 which also keeps secondary and supplementary alignments, this leads to much tidier repeat counting and reduced background repeat counts.

I propose changing filtering from -F 4 to -F 2308.

Thank you.

fritzsedlazeck commented 2 years ago

Thanks Heather thats a great suggestion!

HJeffery commented 2 years ago

Thanks Fritz!