Hi everyone,

I am using the mirdeep2 quantifier module the quantify the miRNA expression with the default parameters.

As some miRNA can be mapped to multiple locations with different counts number, I am confused at how to determine the real counts number:

eg:

#miRNA         read_count    precursor
bta-let-7a-3p    994    bta-let-7a-1
bta-let-7a-3p    994    bta-let-7a-3
bta-let-7a-5p    230845    bta-let-7a-3
bta-let-7a-5p    231026    bta-let-7a-2
bta-let-7a-5p    231087    bta-let-7a-1

we can see that bta-let-7a-5p is mapped three times with slightly different number, so how should i choose the counts number? I would like to make a reads counts matrix for all the libraries I sequenced, which need a unique number for each specific miRNA.

Thanks.