I'm working with microRNA, I have miRNA-Seq from different tissue and I want to perform DEA among them, but only considering a small genomic region. I aligned my reads against my reference, and I visualized them on IGV. The peaks I see do not correspond to any annotated miRNA for my reference genome, so I have not an annotation. In order to perform DEA, I want to create a Count Table containing the number of reads for each peak I see in my region of interest (I want to use it for DESeq2) . How can I do this peak-calling operation for mapped miRNAs? I have only the BAM and SAM files derived from the alignment (performed with Bowtie2) and the reference genome (FASTA). Thanks in advance!