The core facility for RNA-Seq used cuffmerge to generated a merged.gtf file (i.e. a merged assembly file).
I wanted to know what the difference was using the merged.gtf file to get raw counts using subread from .bams vs. using the most recent ensembl .gtf for my species.
When I run the subread with the merged.gtf file, I only get cufflinks IDs for the gene names with no gene symbols. Does anyone know if there is gene symbol or shortname information in the merged.gtf?
Thanks in advance!