I am using the latest mice reference genome (GRCm39) for small RNAseq/miRNA-seq analysis. MiRBase database doesn't have any GFF/GTF file for the mouse mature-miRNA/loop-miRNA.
I just have mature-miRNA and loop-miRNA fasta sequences from MiRBase. How I can use the STAR tool to generate genome index and GeneCounts by using fasta miRNA fasta file? I want use STAR for generating read counts for each miRNA by using --quantMode TranscriptomeSAM GeneCounts.