Calculate the TPM values after running Combat-seq

[Xunzhi Zhang]

Hello,

In the output of RSEM, there are "length" and "effective_length" columns for each transcript. I wonder which one is used when RSEM calculates the TPM values.

I ran Combat-seq on the expected counts from RSEM to adjust the batch effects. Then I want to convert the results into TPM values. I noticed that the effective lengths vary among the samples, so I wonder if I should use the lengths for TPM calculation, since the lengths keep the same.

Thank you very much!