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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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Parameters related to Multimapping genes count #350

Closed zmf0621 closed 1 year ago

zmf0621 commented 1 year ago

Hello dear author, I noticed that the parameters used when gene counting with FeatureCounts are "-M" and "--primary", in the final result I got some key genes are pseudogenes, which makes me have to look back at this parameter Because I don't know whether this setting can distinguish the parent gene from the pseudogene. Hope to get your answer, this is very important to me.

cziegenhain commented 1 year ago

Hi,

Sorry for the slow reply. In principle there could be highly similar reads that are subject to multi-mapping but assigning them to a putative parent gene may not be trivial and is not implemented in zUMIs.

Best, Christoph