Hi there, I’d like to calculate TPM from my HISAT2 output files (.bam). I’ve used Stringtie and provided a reference gtf file and have successfully gotten the TPM calculations. However, I realized that because Stringtie also predicts new transcripts, I’ve gotten TPM values for the predicted transcripts as well.
Is there another tool I could use that doesn’t include the predicted transcripts, or could I scale up the TPM values of the known transcripts after removing the TPMs of the predicted transcripts? I’m aware of Salmon/Sailfish/Kallisto but would prefer to use the HISAT2 files which were aligned to a genome rather than transcriptome for consistency.
Thanks in advance!