Question: Is there a way where we can convert TPM to raw read count?
0
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5 months ago by
Researcher50
Researcher50 wrote:

I have a GEO dataset which only has log2TPM values but for a downstream analysis I would require only its raw read count. Is it possible to back calculate the raw read count from TPM values? Kindly guide.

ADD COMMENTlink written 5 months ago by Researcher50
1

Short answer: No.

Long answer: No, you would need the exact code that the authors used and the effective length they used for gene length normalization.

It would be much safer to simply download the raw fastq files and then process them to get a raw count table. See Fast download of FASTQ files from the European Nucleotide Archive (ENA)

ADD REPLYlink modified 5 months ago • written 5 months ago by ATpoint36k

Thanks @ATpoint for explaining it well.

ADD REPLYlink written 4 months ago by Researcher50
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