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:
#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.