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counts reads for miRNA mapped againt mirbase

Hello,

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 ?

Thanks

mirna-seq
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written by jonessara770 jonessara770

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.

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written by GenoMax GenoMax

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