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alexdobin / STAR

RNA-seq aligner
MIT License
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Dose STAR avoid mapping to low complexity region? #1559

Open linpei26 opened 2 years ago

linpei26 commented 2 years ago

Hello Alex and everyone!

I wish to know if STAR by default will avoid mapping reads to low-complexity region in the genome? (For example, a read consist of 'A' mostly will NOT be mapped?)

or we just simply ignore those multi-mapping reads to achieve the same goal?

BTW, dose STAR only considered uniquely mapped reads when counting reads for each gene? Thanks in advance!

With best regards,

Pei

linpei26 commented 2 years ago

With --quantMode GeneCounts option STAR will count number reads per gene while mapping. A read is counted if it overlaps (1nt or more) one and only one gene.

alexdobin commented 2 years ago

Hi @linpei26

there is no special consideration for low-complexity regions, but if a read maps to "too many" loci, it's not output. --quantMode GeneCounts option only counts uniquely mapping reads.