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

As the title...

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

rna-seq tpm deg
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updated by ATpoint ATpoint • written by wensulin93 • wensulin93

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

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written by antonioggsousa antonioggsousa

Thanks very much for your reply!

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

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written by wensulin93 • wensulin93

1 answer

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.

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written by ATpoint ATpoint

Thanks very much for your reply!

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

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written by wensulin93 • wensulin93

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