6 weeks ago by
I think everybody has essentially conveyed the right idea: you would typically have those (TPM versus FPKM) with different quantification methods (transcript quantification versus gene quantification).
If you have read counts for transcripts for a transcript TPM value, you could add those at the gene level (which is how you could then calculate FPKM values from the counts provided alongside your TPM values, with your transcript quantification). However, that involved assignment of ambiguous reads between transcripts and multi-mapped reads (which could be between genes). So, your FPKM values with unique reads won't be the same.