I have not done miRNA data analysis before, I have a small question regarding miRNA read mapping. The miRNAs are generated either by cleaving off from a mRNA or from a translated hairpin structure from a part of genome. They function by complimentary base pairing with mRNA of certain gene.
If we assume that the miRNA generated is from a genomic region, when we align this miRNA reads to the genome, ideally this read should map to the genomic position where it is originated and also to the corresponding exonic region which it is supposed to form a complimentary base pairing. Hence, the miRNA that forms base pairing with mRNA, should map to the two locations in the genome. I would like to know if my understanding is correct.
And also the miRNA will map to the exonic portions of the genome. ??