Newbie here. I am trying to use featureCounts to assign reads to features (exons). My reference is E. Coli. I downloaded the gtf file from here: https://www.ncbi.nlm.nih.gov/genome/167?genome_assembly_id=161521 I am noticing that my % assigned is very low after running featureCounts. However, I also noticed in the gtf file there are only ~300 exons listed. Is this correct for E. coli? I can't find any resources online to help me with this. Here is the featureCounts command I run:
featureCounts -p -t exon -g gene -T 16 -s 2 -a GCF_000005845.2_ASM584v2_genomic.gtf -o counts.txt input_file.bam
Maybe I am not downloading the correct gtf file but I need this exact strain.