Im cureeently working on miRNA data and i need to know the known and novel mirnas present in my samples. im using mirdeep2 for mapping and quantification. Here mirdeep2 is asking input files colapse and maaped files which i have provided it which i got via mirddep2 mapper and genome file which i have downloaded from ncbi, after providing everything im getting error. Please, can anyone gere guide me through it.
This tutorial has very good example data, and a workflow template that you could adopt: Whole transcriptome analysis of Arabidopsis thaliana