Hello!

I am currently analyzing a set of RNA-seq data. I first used StringTie to calculate the TPM values of reads that are mapped to the genome (a non-model organism). Then, for the ~5% of reads that were not mapped to the genome, I used Trinity to *de novo* assemble the reads and then used Kallisto to calculate the TPM of these transcripts.

Are the TPM values calculated by StringTie and Kallisto comparable? For example, can I combine the two lists of TPM values and look at the top 30 expressed transcripts?

Thank you very much!
No, I don't think concatenating your TPMs like this is a good idea: both data sets are normalized to 1million, however the number of reads is very different between them. 

If you want to do something like this, I would:

1) map reads to genome

2) used unmapped reads to assemble transcriptome

3) extract / get transcripts from genome

4) concatenate assembled transcriptome and extracted transcripts into new reference transcriptome

5) use kallisto to estimate TPMs / counts for new reference transcriptome