Calculating TPM from HISAT2 (bam) files

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!

Hi @julsies, Stringtie > Advanced option > Output gene abundance estimation file? The default setting is No. Hope this helps.

Hi @julsies Stringtie also has Use Reference transcripts only? option, and the default setting is No.
Kind regards,

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Thank you, can’t believe I missed that!