I have paired end RNA-Seq reads that I aligned to my reference genome using HISAT2 (alignment mostly >90%) and obtained BAM files, as a result. When I tried to obtain count information for these BAM files using the annotated file of the same build of the reference genome, I find that the resulting file has count values of 0, throughout.
I used exon as the GFF feature, excluded chimeric fragments, only allowed fragments with both reads aligned and allowed exon-exon junctions. The rest were all default settings, including not counting multimapping reads. I could see that there was a junction counts file having values for counts, though.
This is my counts summary : Assigned 0 Unassigned_Unmapped 6571202 Unassigned_MappingQuality 5083205 Unassigned_Chimera 0 Unassigned_FragmentLength 0 Unassigned_Duplicate 0 Unassigned_MultiMapping 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_NoFeatures 64827954 Unassigned_Overlapping_Length 0 Unassigned_Ambiguity 0
Could someone help me with this, please?