miraligner has an extra module to help with cross-mapping events

The problem when annotating miRNAs using only the miRBase database, it is that sometimes you could mis-annotate a sequence. An example: you have a sequence mapping onto a miRNA with a mismatch, but when you map against the genome, you find that the sequence has different perfect match. For that we coded crossmapping.py, which uses the output of miraligner and gives you a clue about when a miRNA could be mis-annotated.

Read more here:

miraligner wiki