What tools are better than Cuffdiff for differential expression analysis

Question

[tunl]

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!

Answer 1

[GenoMax]

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

[tunl]

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!

[GenoMax]

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