Question: counts reads for miRNA mapped againt mirbase
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gravatar for jonessara770
13 months ago by
jonessara770130
jonessara770130 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 • 550 views
ADD COMMENTlink written 13 months ago by jonessara770130

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 13 months ago by genomax64k
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