Transcript-level differential expression using DESeq2
1
0
Entering edit mode
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
1
Entering edit mode
@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
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 211 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6