Hi Biostars, I used featureCounts to generate the counts table for the DEG analysis of my RNASeq data. I didn't count multi-mapping reads, but one of my libraries has 33% multi-mapped reads. I am afraid if I exclude the multi-mapping reads I will end up loosing a significant portion of the information. Please suggest me whether I should include or exclude multi-mapping reads in featureCounts. Whether these settings will make significant changes in the DEG analysis result?