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.
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 .