I am working on a set of RNAseq samples. I am using featureCounts from the subread package in order to count fragments (not reads) falling into genomic features. I am using the command line option "--ignoreDup" to exclude duplicate reads. The results seem somewhat strange...
Here is the summary file provided by featureCounts for two samples:
All samples were processed in the same way and same commands were used to run featureCounts. Why does one sample have 0 unassigned duplicates and the other 68111548? This difference seems so black and white that I am afraid there is an error somewhere. What exactly does it mean to have unassigned duplicates?