Generating a New GFF file from a previously merged Stringtie File

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I have an out there question. The genome I am working with has a very poor annotation, so on the first round of sequencing samples I ran Stringtie to identify novel transcripts, and as anticipated, after BLASTing the sequences of a lot of these transcripts they were actually genes. So I am done that work to correlate MSTRG numbers to genes. I now have a new set of samples and would like to use the new merged annotation I created as the reference annotation, but still have it search for novel transcripts. The issue is when I do that it reassignes the original MSTRG numbers and I no longer have a file that correlates the sequences to genes.

I need to either create a new GFF replacing the original MSTRG with the genes I identified, OR need to find a way to have Stringtie NOT reassign MSTRG numbers.

Does anyone have any suggestions on how to approach this, either option?

Thank you!

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Hi @KMKLOHONATZ

To use what you have already assigned, you would need to create a new reference annotation file, then incorporate it into the analysis at the usual step where known annotation is used.

Or, you could decide to assign/map new identifiers after the analysis is completed. Meaning, do your mapping after you have DE results.

The second is probably easier, but you could review a tool like this if you want to try the first → Maker genome annotation pipeline