I aligned my miRNA-Seq againt mirbase by bowtie. I would like to count the reads aligned to each miRNA. is there any tools specific for this ?
Since miRNA's are small your alignment should cover most of the length of the miRBase entry you could do samtools view your.bam and then cut the third field out (which should be the name of miRBase miRNA) and count those hits.
samtools view your.bam