What to use after Salmon

Question

[dina.hesham139]

Hi, I'm recently using Salmon for rice RNAseq analysis. Well, after obtaining normalized TPM, How can I proceed? I used to use tuxedo pipeline for expression analysis, what kind of tools can I use after Salmon? Thanks

Answer 1

[John]

Mmm, salmon and rice... sounds like the recipe for a good sushi.

All you need now is a little wasabi: https://github.com/COMBINE-lab/wasabi

And then you can use Sluth from the Kallisto guys to do the downstream stuff: http://pachterlab.github.io/sleuth/

There's also SalmonTools: https://github.com/COMBINE-lab/SalmonTools

[andrew.j.skelton73]

Additionally to what John said, you can also read Salmon results into DESeq2 using tximport for a gene level analysis.

[dina.hesham139]

Hilarious :D Thanks so much!!