I've got a question. Can we compare the quantification files from Salmon and from HTseq-count?
I mean, Salmon quantifies reads over transcripts and HTSeq-count can quantify reads over exons. So, is it meaningful to say : "the exon AT5G00000.exon.1 gets 14 reads (HTSeq count) and the isoform AT5G00000.1 get 114 reads (Salmon) , then, these tools quantify differently and there is a significant difference between reads estimated by Salmon and HTSeq". ??