I have a question in how to interpret StringTie results using the protocol published in Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown:
O followed the protocol assembling transcripts (step 3), merging all results (step 4) and restimating transcript abundances (step 6). After this last step, I wanted to know if an assembled transcript was present in normal and/or tumoral conditions.
So, I looked in the merge file and I identified annotated transcripts and potential new assemblies . For annotated transcripts I could identify where they were assembled (normal and/or tumoral condition) searching the ENSEMBL ID in the GTF file of each sample created in step6. However, I could not do the same thing for the new assemblies.
My question is: how can I know if a new transcript was assembled in a specific or both conditions?