After RNA seq, alignment, counting, and normalization of the counts (TPMs), finally I have a document representing a tissue at a particular condition with all the transcript IDs and TPMs. I have 2 questions:
- If I just want to know how many transcripts are expressed in that tissue at the particular condition (the total number of transcript expressed), which transcripts I select from the list? The ones that have TPMs more than 0 or a larger number?
- How can I select a TPM cut-off value for further analysis of the more expressed transcripts?
Thank you very much