Hi! I am performing gene expression analysis using two pipelines:
- Pipeline 1 : HISAT2 + htseq-count
- Pipeline 2 : STAR + RSEM
I obtained an higher mapping rate with STAR compare to HISAT2 and RSEM assigned more reads to genes compared to htseq-count.
However when I looked at the number of genes with more than 5 counts, I observed that I got an higher number of genes with htseq-count than RSEM.
I was wondering why RSEM identified less genes than htseq-count.