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.

Hi liran0921 and others, I need some help in quantifier module of mirdeep2. I need to quantify some deep sequencing reads for differential expression analysis. I assume i should just go ahead with quantifier module with matrue , precursor and read sequences (as per the documentation)?!. Or should i map them to genome and then proceed with quantification?

P.s: the reads are already adapter trimmed.