Question: counts reads for miRNA mapped againt mirbase
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gravatar for jonessara770
2.6 years ago by
jonessara770210
jonessara770210 wrote:

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 • 1.1k views
ADD COMMENTlink written 2.6 years ago by jonessara770210

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.

ADD REPLYlink written 2.6 years ago by genomax90k
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