Salmon: Any downstream DEA tools which uses abundance estimate variation information?

Question

[Thomas]

Dear Biostars community,

I was just wondering if there are any differential expression analysis tools which can be used downstream of Salmon, which incorporates abundance estimate variation information when either the --numBootstraps or --numGibbsSamples are used when running salmon quant?

The salmon documentation states the following:

Such estimates can be useful for downstream (e.g. differential expression) tools that can make use of such uncertainty estimates.

Do we know of any tools which will incorporate this transcript abundance estimate variation information when calling differential expression at the transcript-level i.e (DTE - differential transcript expression).

I think Sleuth does something along these lines with kallisto output, but I was just wondering if there was any tools that processed Salmon output in a similar manner. I have looked at the vignette, and I do not think DeSeq2 (version 1.22.2 at the time of writing) does this, unless I am mistaken?

Many thanks

[h.mon]

You can use wasabi to prepare Salmon output to be used with sleuth.

Answer 1

[ATpoint]

Fishpond is designed to do exactly this: https://bioconductor.org/packages/release/bioc/html/fishpond.html

This was a collaboration between the Love lab (DEseq2 etc) and the Patro lab (salmon developers), see https://academic.oup.com/nar/article/47/18/e105/5542870

Answer 2

[Kevin Blighe]

Just updating this thread with a new answer:

tximport does this, too: Salmon with inferential replicates.

Kevin