Dear all, I use Subread in Bash for mapping and FeatureCounts for count quantification for my RNASeq data. I have used the same pipeline for other RNASeq datasets in the past and FeatureCounts gives count output for all the genes in the annotation file.
Recently I performed RNASeq 150 bp paired-ends reads in rice (Illumina). However, this time, after running featureCounts the count output file contained only 24000 genes out of total 42000 genes in the annotation file. I cannot understand why is it so? Does it suggest that mapping failed for the 18000 ignored genes? Does it suggest PCR amplification-based duplicated reads?
Can someone explain why is it so?