Gene id duplication caused by prepDE3.py

[jgreen51515]

Hello. We ran StringTie and then used prepDE3.py to get the gene counts and are seeing cases like the following where the gene id from the reference genome is mapped to 2 novel genes found by StringTie.

MSTRG.1|Zm00001d027230 MSTRG.2|Zm00001d027230

This is giving us 2 different sets of expression calls for the gene Zm00001d027230. We want only 1 set of expression calls for Zm00001d027230. It'd be fine if the gene was named like MSTRG.1|MSTRG.2|Zm00001d027230. Can you help with this issue?

Thanks, Julie