Differences between number of expressed genes obtained with RSEM and htseq-count
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12 months ago
concetta ▴ 10

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

rna-seq rsem htseq-count gene abundance • 368 views
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