zUMI counts multi-mappers, is there an option to only allow uniquely mapped reads counted?

[MengjunWu]

Hi, I noticed during counting by featureCount, zUMI allows multi-mapper and without fractional counting. I was wondering if there is an option which allows the user to flexibly choose count multi-mapper or uniquely mapped reads?

Thanks a lot!

Best, Mengjun

[cziegenhain]

Hi Mengjun,

You can choose to count multimappers or only count uniquely mapped reads via the primaryHit option. https://github.com/sdparekh/zUMIs/blob/main/zUMIs.yaml#L79

Best, Christoph

[MengjunWu]

Hi Christoph,

thanks for quick response! If I understood correctly, the primiaryHit still include multi-mapper but only count once (the primary hit), which means in featureCount the "primaryOnly" option was set to be TRUE? But this will still include multi-mappers. What I was wondering is if one could set the "countMultiMappingReads" option to be FALSE in featureCount function, so one will only count reads that mapped only once in the genome.

Or if I set primaryHit to be FALSE, the "countMultiMappingReads" in zUMI will also be set to be FALSE in zUMI?

Many thanks, Mengjun

[cziegenhain]

Hi Mengjun,

Yes, if you set primaryHit: no in zUMIs, you will only get counts from uniquely mapped reads.

[MengjunWu]

Great, thanks a lot!