Can I use ALFRED transcript counting for TPM calculation?

[kosmintema]

Thank you for your work on ALFRED — it's a great tool!

I’m working on a transcript quantification pipeline, and I’m interested in using ALFRED’s transcript-level counting as part of my TPM (Transcripts Per Million) calculation. I wanted to ask:

1. Is it appropriate to use ALFRED’s transcript counts directly for TPM computation?
2. Are there any caveats or assumptions I should be aware of when doing so?

[tobiasrausch]

Alfred currently outputs raw gene counts or FPKMs using the alfred count_rna subcommand. You can convert FPKM to TPM for gene i using TPM(i) = ( FPKM(i) / sum ( FPKM all transcripts ) ) * 10^6