I need to run featurecounts two separate times, each with a different annotated reference genome.
Q1. My first genome is not a common one, there is a genbank file but no gtf file. I see mixed reviews on conversion tools…
Q2. My second genome I got a gtf file from ensembl bacteria, just wondering if I need to convert this to UCSC format before featurecounts or just make sure it matches my bam output files from bwa-mem mapping step? My gtf file has “chromosome” in the first column, and “gene_id” in the attributes column whereas my bam files look different (attached here).
Appreciate any advice on this