Question: which option is better for DESeq2 analysis: salmon or htseq-count?
gravatar for Lila M
21 months ago by
Lila M 780
Lila M 780 wrote:

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!

rna-seq salmon de htseq-count • 1.4k views
ADD COMMENTlink modified 21 months ago by kristoffer.vittingseerup2.0k • written 21 months ago by Lila M 780
gravatar for kristoffer.vittingseerup
21 months ago by
European Union
kristoffer.vittingseerup2.0k wrote:

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.


ADD COMMENTlink modified 21 months ago • written 21 months ago by kristoffer.vittingseerup2.0k

Thank you for this fantastic answer, very informative!

ADD REPLYlink modified 21 months ago • written 21 months ago by Lila M 780
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