Issue with StringTie--not picking up reference gene IDs

[sanchari24]

Hello, I am using StringTie for RNA-seq analysis and want to use DESeq for differential gene expression analysis.

After running the command for creating ballgown input files, I used PrepDe.py to extract the gene_count matrix. It is not picking up most of the gene annotations and using default StringTie IDs. Is there a way to work around the problem ?

Thanks