I've already posted a question about Salmon earlier , but this one is totally different
I used two different mappers like Hisat2 and Salmon to map my reads . I got good overall read mapping reads with both of them.
I used HTSeq-count to quantify my mapped reads from Hisat2. But the quant.sf file of Salmon gave me different results : on the one hand, counted reads are quite similar lbetween Htseq-count results and quant.sf file , but on the other hand, there could be a factor 40 between reads counted from Salmon and HTSeq-count for the same exon. Moreover, HTSeq-count will count 0 read for an exon while Salmon will count 15 reads for the same one. I really don't understand these results. I found some papers talking about that but nothing that gave me a good answer..
In addition, I'm gonna show you my results (just the 10 first lines) :
AT1G01010:exon:1 1 AT1G01010:exon:2 2 AT1G01010:exon:3 0 AT1G01010:exon:4 2 AT1G01010:exon:5 2 AT1G01010:exon:6 3 AT1G01020:exon:1 0 AT1G01020:exon:10 0 AT1G01020:exon:11 0 AT1G01020:exon:12 1
Salmon quant.sf (I've deleted the 3 middle lines of the file to get a better visualization)
AT1G01010.1 34 AT1G01020.2 43.6719 AT1G01020.6 13.3601 AT1G01020.1 54.2279 AT1G01020.4 0 AT1G01020.5 12.2951 AT1G01020.3 21.4449 AT1G01030.2 8.79053e-05 AT1G01030.1 19.9999
Is it due to the expectation-maximization algorithm of Salmon that some transcripts from HTSeq-count (for example AT1G01010:exon:4 is not found into the Salmon's file?