Question

Transcript-level differential expression using DESeq2

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Rain Yi • 0

@rain-yi-24046

Last seen 7 months ago

Dear DESeq2 community,

I am just wondering whether I can use DESeq2 to perform transcript-level differential expression with Salmon quantification data? And if I can, is that essential to include bootstrap when using Salmon? I saw a tutorial said DESeq2 will not work if one want to do transcript-level differential expression, just curious whether it is true or not.

Thanks.

deseq2 transcript-level differential expression • 292 views

ADD COMMENT • link updated 12 months ago by Michael Love 34k • written 12 months ago by Rain Yi • 0

score 1 · Answer 1 · 2020-08-25

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Michael Love 34k

@mikelove

Last seen 22 hours ago

United States

We have two relevant papers from my lab here:

This is a benchmark that explores gene level tools used to perform DTE (the benchmark follows the workflow section on DTU):

https://doi.org/10.12688/f1000research.15398.3

And this is a new Bioconductor method/package we developed (based on ideas from SAMseq) for performing DTE. The method is called Swish and the package is fishpond.

https://doi.org/10.1093/nar/gkz622

I really like this method, it’s fast, easy to use, has very good error control and sensitivity across a range of sample size, and the vignette shows how to make results tables and plots just like in DESeq2 (counts plots and MA plots).

https://bioconductor.org/packages/release/bioc/vignettes/fishpond/inst/doc/swish.html

ADD COMMENT • link 12 months ago Michael Love 34k

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Thanks Michael. So what you suggested is using fishpond to do transcript-level differential expression instead of DESeq2?

ADD REPLY • link 12 months ago Rain Yi • 0

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Yes, it is exactly designed for this. Give it a shot and let me know if you have any questions.

ADD REPLY • link 12 months ago Michael Love 34k

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Thanks Michael! I'll try it out. One more question, can I use DESeq2 for transcript-level differential expression if the read quantification data were generated by StringTie since this is an alignment-based aligner? Or I still have to use fishpond?

ADD REPLY • link 12 months ago Rain Yi • 0

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With StringTie they don’t have a measure of quantification uncertainty so you can’t use Swish. You can use DESeq2 then.

ADD REPLY • link 12 months ago Michael Love 34k