I am doing miRNA Seq analysis and I am new to it. I have indexed my genome using bowtie and mapped it. Inorder to identify the known or novel miRNAs, I thought of using miRDeep2 tool.
I read a protocol saying you need mature miRNA of closely related species (eg: Gorilla) for carrying out miRDeep2 tool.
What is the purpose of having mature miRNA of other species and also genome and mature miRNA of species interested??
Thank you in advance.