I aligned some paired-end RNA-seq data using STAR and then used featureCounts on the output .bam to assign them to genes. However I'm really confused as the output of featureCounts shows that I have more fragments (read-pairs) than the number of total input reads (I'm assuming also read-pairs/fragments) in the STAR output.
Number of input reads | 45661688 Average input read length | 199 UNIQUE READS: Uniquely mapped reads number | 41983291 Uniquely mapped reads % | 91.94%
|| Paired-end reads are included. || || Assign fragments (read pairs) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Read re-ordering is performed. || || || || Total fragments : 49756690 || || Successfully assigned fragments : 36826889 (74.0%) ||
45661688 vs 49756690... where have these extra ~4 million reads come from? Also, aren't multimapped reads excluded from the .bam STAR output anyway so really it is 41983291 vs 49756690? Anyone any ideas?? Thanks!