search

sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
269 stars 67 forks source link

yaml multimappers options #301

Closed mlizio closed 2 years ago

mlizio commented 2 years ago

Hi,

Does setting 'primaryHit: yes', the default, mean that featureCounts counts unique alignments as well as the best alignment for reads mapping to multiple locations?

I am running zUMIs on a mixed human and mouse single cells dataset, and wanted to have a breakdown of what fraction of the identified barcodes correctly labels cells from one genome only, compared to barcodes labelling mixed genomes.

In other words, how do I distinguish the case of a read that maps equally well to both human and mouse from the case of a read that maps to only one genome? Would I have to set 'primaryHit: no' to avoid multimappers altogether?

thanks

mlizio commented 2 years ago

I did solve this by trying both ways and comparing log files and results. Closing the issue.