I am using miRDeep2 to predict novel miRNAs across multiple samples for differential expression analysis. Here are some of my questions:
- How do I make a list of novel miRNAs across samples?
- In each sample, there are identical mature miRNAs derived from different loci, since I'm only interested in the expression profile of mature miRNAs, not their genomic location, I have to remove the redundant predictions from the list. How can I do this?
- How to name my newly discovered miRNAs?