Differences between number of expressed genes obtained with RSEM and htseq-count
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.
Thank you!
Concetta
• 1,330 views
•
link
written
by
concetta •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
galaxy and RNA seq
written by nmozdoori •
-
Current best practice for alignment and quantification for downstream analysis in DESeq2
written by yura.grabovska •
-
STAR pair-end gene count discrepancy vs. RSEM
written by anon •
-
Comparison DESeq results using different model
written by concetta •
-
Large Count Discrepancy of Key Gene Between STAR and HISAT2
written by dk0319 •
-
Counting reads over genes with summarizeOverlaps
written by concetta •
-
Different mapping results between HISAT and TopHat
written by concetta •
-
How to normalize gene expression with CPM
written by concetta •
-
many intronic reads and no features counts in 3' RNA-seq sequencing
written by concetta •
-
STAR-HT-Seq/featureCount got much more gene expression count than RSEM did
written by CY
