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What to use after Salmon
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13 months ago
Egypt

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

RNA-Seq • 1.5k views
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15 months ago
John 12k
Germany

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

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

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Hilarious :D Thanks so much!!

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