I am analyzing small RNA data currently, but there are some questions about Rfam and mirdeep result? could someone give me some advice, thanks!
1. I use bowtie to map my reads to Rfam data to annotate the other ncRNA except miRNA, but the Rfam data including ncRNA from many species, I don't know just map my reads to the whole Rfam database or just the data of the species I study?
2. I use mirdeep2 to predict the novel miRNA of each sample, but I want to do the differential expression of novel miRNA between different samples, but the name of novel miRNA given by mirdeep are really different, I don't know how to deal with it.