Question: Can Kallisto be followed by DESeq, EdgeR or Cuffdiff?
1
gravatar for Annika Forsingdal
3.2 years ago by
Copenhagen, Denmark
Annika Forsingdal210 wrote:

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

rna-seq • 4.5k views
ADD COMMENTlink modified 3.2 years ago by Rob2.8k • written 3.2 years ago by Annika Forsingdal210
2

Yes, you can.  Some thoughts on the matter:

http://f1000research.com/articles/4-1521/v1

ADD REPLYlink written 2.9 years ago by mark.robinson100

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

ADD REPLYlink written 3.2 years ago by lakigigar200
3
gravatar for Rob
3.2 years ago by
Rob2.8k
United States
Rob2.8k wrote:

(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.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Rob2.8k

Thank you. 

ADD REPLYlink written 3.2 years ago by Annika Forsingdal210
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