I used STAR to align my reads (brain samples) to human reference genome. Getting good unique mapping rates (~70-90%).
However, when I use featureCounts I get really low assignment rates.
Here is an example command
featureCounts -p -t exon -g gene_id -s 2 -T 16 -a gencode.v38.annotation.gtf -o counts.txt Aligned.sortedByCoord.out.properPairs.bam
Any ideas why my assignment rate is so low? Should I be mapping to genes instead? Even if I do that I only get around 26% assignment which is better but still very low.