I am using featureCounts to try and create a count table for some RNA-Seq data I collected using an Oxford Nanopore platform. I have .sam files aligned with minimap2, and am running the following command to try to get a count table:
featureCounts -a knownGene_v36.gtf -o countFile *.sam -L
Both the GTF file I am using, and the reference genome that the alignments were generated off of, are from UCSC table browser, HG38, knownGene, GENCODE v36.
Running this in the directory with the .gtf prints out an extremely long list of errors like the ones below:
ERROR: Unable to find chromosome 'hg38_knownGene_ENST00000407684.1' in the SAM header! ERROR: Unable to find chromosome 'hg38_knownGene_ENST00000401533.7' in the SAM header! ERROR: Unable to find chromosome 'hg38_knownGene_ENST00000474095.1' in the SAM header! ERROR: Unable to find chromosome 'hg38_knownGene_ENST00000506070.1' in the SAM header!
It appears to be outputting this for every gene. I originally thought there was a problem with the way the GTFs are formatted, because it's referring to the genes as chromosomes, but featureCounts seems to be pretty good about checking the gtf format before the program runs. I really don't know what I'm doing wrong- is it possibly an alignment setting that makes my SAM files improperly formatted?