Differences between number of expressed genes obtained with RSEM and htseq-count

Question

[concetta]

Hi! I am performing gene expression analysis using two pipelines:

1. Pipeline 1 : HISAT2 + htseq-count
2. 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.

Thank you!

Concetta