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!