Differential expression tool that can take TPM as input?

Question

[Tye Kahn]

Due to my analysis, I need to use TPM as input for my differential expression analysis.

I tried to use both DESeq2 and EdgeR by skipping both normalization and independent filtering steps. Even so, the number of DEGs is 3 times lower than using the original raw data (in DESeq2).

Does any of you know of any tool that allows using TPM as input for this kind of analysis?

Answer 1

[ATpoint]

https://support.bioconductor.org/p/126817/

Please also use the search function and google as this has been addressed literally dozens of times.

[Tye Kahn]

Already searched for it, but none of the results was informative. About the link, CPM, unlike TPM, does not take gene length into account. Do you think that may have any effect on the results? I would think so.

[Kristoffer Vitting-Seerup]

the length normalisation does not make to much of a difference as it is hopefully the same in all samples - and you only compare the sample gene between samples. Meaning the results you got for CPM should be usefull.