Explore Novel miRNAs

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 (Image read_mapping_16_n_p). 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 (Image graph_track_16_n_p) and Identify Graph Treshold Areas (Image graph_threshold_area_16_n_p) to only consider sequences expressed above a user defined level.

Image potential_novel_mirna_region
Figure 33.31: Region in the human reference genome, with high coverage of reads that could not map to the miRNA reference database.

Next, to extract the sequence in the regions of high coverage use the tool Extract Annotations (Image extract_annotations).

Finally, the tool Predict Secondary Structure (Image rna_secondary_structure) can be used to check if the structure matches the expected hairpin structure of miRNA precursors.

Image precursor_mirna_secondary_structure
Figure 33.32: Sequences extracted from regions with high coverage and annotated with predicted secondary structure.