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STAR mapping #80

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RamilNurtdinov opened this issue Aug 6, 2023 · 0 comments
Open

STAR mapping #80

RamilNurtdinov opened this issue Aug 6, 2023 · 0 comments

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@RamilNurtdinov
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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
.
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@RamilNurtdinov