Question: What tools are better than Cuffdiff for differential expression analysis
0
gravatar for tunl
2.9 years ago by
tunl60
tunl60 wrote:

I heard that Cuffdiff is no longer considered as a very good tool for differential expression analysis.

I am wondering what the major issues are in Cuffdiff ?

What tools are better than Cuffdiff for differential expression analysis?

Thank you very much for your advice!

ADD COMMENTlink written 2.9 years ago by tunl60
3
gravatar for genomax
2.9 years ago by
genomax75k
United States
genomax75k wrote:

If you are doing alignment following by counting the reads to get counts then DESeq2, edgeR. If you are comfortable with "mapping" then Salmon, Kallisto.

See this thread for more on alignment versus mapping: Alignment and mapping

ADD COMMENTlink written 2.9 years ago by genomax75k

Thank you for your advice!

So you think DESeq2 and edgeR are more accurate than Cuffdiff?

They are faster than Cuffdiff.

But Cole Trapnell (Cuffdiff author) believes DESeq and edgeR (the tools that test raw gene-level counts) are less accurate than Cuffdiff, since they assume that isoforms have the same length.

So are there some known issues with Cuffdiff?

Thanks a lot!

ADD REPLYlink written 2.9 years ago by tunl60
1

Results of these tools are not the end points of an investigation. You would be independently testing the hypothesis generated to confirm them.

ADD REPLYlink written 2.9 years ago by genomax75k
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