FeatureCounts: All Features Either Unassigned_Unmapped or Unassigned_NoFeatures

I am currently experiemcing some difficulies counting mapped reads: I have used featureCounts, all features show up as either Unassigned_Unmapped or Unassigned_NoFeatures.
Mapping the reads does not seem to be the issue as the reads could successfully be visualized using JBrowse.

However, I think the issue might be with the GTF file I am using, as no visualization of the annotated reference (GTF from UCSC table browser, converted to GFF3 using gffread) is possible via JBrowse. Where might I find alternative GTF files?

In case anyone else encounters this problem, here is the solution that worked for me:

The gtf file I had used wasn’t ideal which resulted in improper assignment. This could be fixed by trying out different gtf files in JBrowse (after gffread conversion to gff3) and using the one that showed us in the visualization via JBrowse.
Additionally, featureCounts had to be set to look for “gene” instead of “exon”, once again due to the formatting in the gtf file.

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