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alexdobin / STAR

RNA-seq aligner
MIT License
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Does clip5pNbases affect outFilterMatchNminOverLread? #2089

Open johnchamberlin opened 6 months ago

johnchamberlin commented 6 months ago

I'm trying to figure out some unexpected behavior with paired end alignment and overlapping mate pairs. As stated in the title,

Does STAR use the total read length (say, 150+150) to calculate outFilterMatchNminOverLread even if I tell it to softclip a portion with clip5pNbases? Does it adjust the 'total read length' if the mate pairs overlap?

Thanks,

alexdobin commented 6 months ago

Hi John,

Lread is adjusted for clipped bases. It's not adjusted for mates overlap, but the number of matched bases is not adjusted either.