which option is better for DESeq2 analysis: salmon or htseq-count?

Question

[Lila M]

Hi everybody!

I have a question and I need your opinion! To carry out RNA-seq analysis, I'm working with htseq-count (python) for a while. Then, I run DESeq2 in R to carry out downstream analysis. But I have been reading for a long time the benefits of using salmon instead of htseq-count. Which one do you think is better for DESeq2 analysis?

Many thanks!

Answer 1

[Kristoffer Vitting-Seerup]

I would definitively go for Salmon (or Kallisto) for three reasons:

1) Isoform/transcript based quantification can handle multi-mapping reads - which otherwise gives a bias in genes with less unique sequences - see this post.

2) Isoform/transcript based quantification tools such as Salmon and Kallisto can perform quite advanced bias corrections meaning you will get rid of some confounding factors (see their respective papers).

3) Analysis of transcript/isoforms (such as isoform switches etc) is a growing field and seems to be quite important in some sitiuations - so why not also enable youself to do that. An option for this could be my tool IsoformSwitchAnalyzeR

P.s. remember to use the tximport R package to import the Kallisto/Salmon with the offset option to pass on the bias corrections to your de analysis.

/Kristoffer

[Lila M]

Thank you for this fantastic answer, very informative!