I have a BAM file that I view locally in IGV browser. Specifically, I am focused on hsa-mir-122. The viewer shows a count of approximately 2591 for this miRNA in my sample. However, when I use featureCounts tool in Galaxy, it only counts approximately 30. I am not seeing this behaviour with other miRNAs that I look at. I am using hsa.gff3 for counting miRNAs that I mapped using hg38. My primary feature type is "miRNA_primary_transcript" and my GFF gene identifier is "Name". Strand specificity is stranded (forwards).
Can anyone help explain why my featureCounts output is not even close to what I can see when the IGV viewer?