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What tools are better than Cuffdiff for differential expression analysis

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!

rna-seq differential expression analysis cuffdiff
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written by tunl tunl

1 answer

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

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written by GenoMax GenoMax

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!

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written by tunl tunl

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

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written by GenoMax GenoMax

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