I'm working with the annotation of Illumina reads against mirBase and I have the reads counts. However this annotation gives me two alignments for the two types of miRNA (5p and 3p), however, when I want to compare my result with published result I found that in the article they don't use this discrimination and the count only the miRNA.
They sum the two result, 5p and 3p, or they choose only one, and why?
In the other hand, I read that first at all they make an alignment to the human genome and after that to the mirBase. Nevertheless, is it possible do the annotation directly from the trimmed fastq to the mirBase?