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