We sequenced miRNA from 12 pig samples. I did the analysis using miRDeep2 tool.
My aim is to find isomiRs for each sample. I have written a perl script to annotate isomiRs for the reads mapped to miRNA . I get the below output. The My doubt is, am I using the correct output file for the analysis? Which read count should I use miRBase.mrd or output.mrd?
I got the following folders and files
1) miRDeep2_output/dir_prepare_signature1345475348 (contains .fa, .arf, .bwt and .ebwt)