Can Kallisto be followed by DESeq, EdgeR or Cuffdiff?

Question

[Annika Forsingdal]

Can kallisto be followed by downstream analysis tools other than Sleuth? E.g. DESeq, EdgeR or Cufflinks/Cuffdiff?

[mark.robinson]

Yes, you can. Some thoughts on the matter: http://f1000research.com/articles/4-1521/v1

[Lior Pachter]

No. Please see my comment here that explains why not.

Answer 1

[Rob]

(Edit:) Yes, you can use the estimated number of reads (appropriately rounded) in downstream analysis tools like DESeq or EdgeR. Of course, Kallisto is built with Sleuth in mind, and so other DE tools won't be able to natively take advantage of e.g. the bootstrapped uncertainty estimates produced by Kallisto. Further, as Lior explains very well here, there are other reasons you should prefer Sleuth over using estimated counts with tools like DESeq or EdgeR; the modeling and distributional assumptions are different.

[Annika Forsingdal]

Thank you.