Hello I am trying to analyze miRNA-seq data but I am having problems with the mapping. I always get pretty much 0 counts with the built in annotation file, so I got one from miRBase. However, I always get an error when I use it, it doesn't even run. I thought the error could have been in the structure of the file, so I downloaded one from GENCODEand compared both structures. They didn't seem different, but the one from GENCODE runs just like the built-in one (runs but gives zero counts). So I have no idea what is going on.

Here are the gff3 structures:

miRBase:

chr1    .   miRNA_primary_transcript    12425986    12426106    .   +   .   ID=MI0021869;Alias=MI0021869;Name=mmu-mir-6341          
chr1    .   miRNA   12426016    12426038    .   +   .   ID=MIMAT0025084;Alias=MIMAT0025084;Name=mmu-miR-6341;Derives_from=MI0021869         
chr1    .   miRNA_primary_transcript    20679010    20679082    .   +   .   ID=MI0000249;Alias=MI0000249;Name=mmu-mir-206           
chr1    .   miRNA   20679017    20679039    .   +   .   ID=MIMAT0017004;Alias=MIMAT0017004;Name=mmu-miR-206-5p;Derives_from=MI0000249           

GENCODE:

chr1    HAVANA  gene    3073253 3074322 .   +   .   ID=ENSMUSG00000102693.1;gene_id=ENSMUSG00000102693.1;gene_type=TEC;gene_status=KNOWN;gene_name=4933401J01Rik;level=2;havana_gene=OTTMUSG00000049935.1           
chr1    HAVANA  transcript  3073253 3074322 .   +   .   ID=ENSMUST00000193812.1;Parent=ENSMUSG00000102693.1;gene_id=ENSMUSG00000102693.1;transcript_id=ENSMUST00000193812.1;gene_type=TEC;gene_status=KNOWN;gene_name=4933401J01Rik;transcript_type=TEC;transcript_status=KNOWN;transcript_name=4933401J01Rik-001;level=2;transcript_support_level=NA;tag=basic;havana_gene=OTTMUSG00000049935.1;havana_transcript=OTTMUST00000127109.1         
chr1    HAVANA  exon    3073253 3074322 .   +   .   ID=exon:ENSMUST00000193812.1:1;Parent=ENSMUST00000193812.1;gene_id=ENSMUSG00000102693.1;transcript_id=ENSMUST00000193812.1;gene_type=TEC;gene_status=KNOWN;gene_name=4933401J01Rik;transcript_type=TEC;transcript_status=KNOWN;transcript_name=4933401J01Rik-001;exon_number=1;exon_id=ENSMUSE00001343744.1;level=2;transcript_support_level=NA;tag=basic;havana_gene=OTTMUSG00000049935.1;havana_transcript=OTTMUST00000127109.1           
chr1    ENSEMBL gene    3102016 3102125 .   +   .   ID=ENSMUSG00000064842.1;gene_id=ENSMUSG00000064842.1;gene_type=snRNA;gene_status=KNOWN;gene_name=Gm26206;level=3            
chr1    ENSEMBL transcript  3102016 3102125 .   +   .   ID=ENSMUST00000082908.1;Parent=ENSMUSG00000064842.1;gene_id=ENSMUSG00000064842.1;transcript_id=ENSMUST00000082908.1;gene_type=snRNA;gene_status=KNOWN;gene_name=Gm26206;transcript_type=snRNA;transcript_status=KNOWN;transcript_name=Gm26206-201;level=3;transcript_support_level=NA;tag=basic         

any idea of what could be wrong?