The Quantify miRNA tool only finds and quantifies the expression of known miRNAs. Here we will describe an approach to exploring novel miRNAs in the data.
First, take the "Unmapped reads" output from Quantify miRNA and use these reads as input to Map Reads to Reference (). To home in on sequences with a decent amount of expression and avoid sequences that map as a result of sequencing errors, we can use the tools Create Mapping Graph () and Identify Graph Treshold Areas () to only consider sequences expressed above a user defined level.
Next, to extract the sequence in the regions of high coverage use the tool Extract Annotations ().
Finally, the tool Predict Secondary Structure () can be used to check if the structure matches the expected hairpin structure of miRNA precursors.