Hi, I am currently running FeatureCounts following mapping meta-transcriptomic data back to various reference genomes. I have predicted genes using prodigal, which outputs into GFF3 format:

JAACZP010000001.1_1 pyrodigal_v1.1.2 CDS 47 1186 127.9 - 0 ID=1_1;partial=00;[…]

I looked to run featurecounts using parameters -t CDS, -p, and -g ID for this file, and it did not map any reads. However, when I use the NCBI downloaded gtf formatted file, appearing as:

JAACZP010000001.1 Genbank region 1 242615 . + . ID=JAACZP010000001.1:1..242615;Dbxref=taxon[…]

SAM file line looks like: D00468:253:HLLHJBCX2:1:1101:9224:1989 77 0 0 * 0 0 NAGAAGGG[...]

I use the exact same parameters, and this file maps 52% of the reads. Is there an error in the way I am passing this file to featureCounts?