Exploring novel miRNAs
One way of doing this would be to identify interesting tags based on their counts (typically you would be interested in pursuing tags with not too low counts in order to avoid wasting efforts on tags based on reads with sequencing errors), Extract Small RNAs
) and use this list of tags as input to Map Reads to Reference
) using the genome as reference. You could then examine where the reads match, and for reads that map in otherwise unannotated regions you could select a region around the match and create a subsequence from this. The subsequence could be folded and examined to see whether the secondary structure was in agreement with the expected hairpin-type structure for miRNAs.