WGCNA from Salmon Output

Question

[Adrij Pawan]

I am working on RNA -seq data analysis, I have quantified my data using Salmon which has given me TPM values for all transcripts. Next, I want to perform Weighted gene coexpression analysis (WGCNA) using transcript TPM values. Is there a direct way to do this? or Do I have to preprocess the TPM values before going the WGCNA?

[jv]

Why TPM? WGCNA is performed with log-transformed gene counts

[Adrij Pawan]

I understand TPM values can not be directly used for WGCNA.However, i wish to know if we use TPM values with some additional processing steps?

[jv]

Please see the following past posts regarding your question:

Is there a way where we can convert TPM to raw read count?

TPM to raw counts