Question

TPM to raw counts

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Sneha • 0

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Last seen 2.2 years ago

India

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CAn we convert TPM values of transcripts to raw counts? 

Can we give them as input to Deseq2?

salmon DESeq2 • 3.9k views

ADD COMMENT • link updated 12 months ago by bella.johnson.2022 • 0 • written 3.0 years ago by Sneha • 0

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I know this is a bit of an old thread, but I used 'tximport' to take my TPM output from Salmon and get the raw counts to then run DESeq2 because I was having the same problem.

Take a look at the tximport vignette to see if it can help.

Cheers!

ADD REPLY • link 12 months ago bella.johnson.2022 • 0

score 1 · Answer 1 · 2022-01-07

If all you have is the TPM values, you can't convert them back to the raw counts. Minimally you would also need the effective length used, for instance.

You also can't feed TPMs into DESeq2.

So if all you have is TPM's, probably the only thing you can do is to use the limma-trend analysis pipeline, ie. log2 your TPM values, and set the trend = TRUE in your call to eBayes()

If you can get access to the fastq's, you may just want to re-align and quantitate so you can get the raw counts yourself. It's getting easier and easier to do these days, especially with tools like salmon, kallisto, etc.