Apologies in advance if this question is very basic =)
I have run
Kallisto using the full human transcriptome dataset
GRCh37-75. This dataset includes both coding and non-coding transcripts, obviously. I would like to further analyse the coding ones. Since the
TPM measurement take into account the total number of transcripts in the dataset, do I need to re-scale/re-calculate the TPM values for each coding transcript using only the coding subset? Is there a difference between this approach or running
Kallisto only on those coding transcripts?
I hope the two questions are clear enough,
Thank you in advance.