Is "TPM" suitable for caculating DEG from different transcriptome researches but one specie

Question

[wensulin93]

As the title...

Is "TPM" suitable for caculating DEG from different transcriptome researches but one specie?

[antonioggsousa]

Hi,

Most of the softwares, such as edgeR and DESeq2, used to estimate DEG will require raw counts and, then, they will apply their own normalization methods.

António

[wensulin93]

Thanks very much for your reply!

I will try these softwares and try to receive raw data!

Answer 1

[ATpoint]

It is not ideal. If you have nothing else than TPM then try limma-trend pipeline. Starting from raw counts is preferable. Please use the search function, this has literally been asked dozens of times before.

[wensulin93]

Thanks very much for your reply!

I will try these softwares and try to receive raw data!