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Published 20 hours ago • verified publisher icon guigolab

STAR mapping

Open RamilNurtdinov opened this issue 1 year ago • 0 comments

HI Emilo

I found funny feature of STAR pair end mapping. 23% of my pair-end read were not mapped. I tried to investigate. I got these unmapped reads and aligned them with UCSC genome browser. I found 100% alignment of both mates but they sufficiently overlaps.

It looks like STAR by default works not properly. We need to set --peOverlapNbasesMin 1 parameter always.

Ramil .

RamilNurtdinov avatar Aug 06 '23 11:08 RamilNurtdinov