Need help in selecting the correct output file from miRDeep2?

Question

[bioinforesearchquestions]

Hi friends,

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)

2) miRDeep2_output/expression_analyses/expression_analyses_04_03_2018_t_07_26_27

• miRBase.mrd

• miRNA_expressed.csv

3) miRNAs_expressed_all_samples_04_03_2018_t_07_26_27.csv

4) miRDeep2_output/mirdeep_runs/run_04_03_2018_t_07_26_27/

• output.mrd

[GenoMax]

For future reference: Editing an original post (even without making any changes) and saving will automatically bump it to main page. No need to create duplicate postings/add fake answers on original post.

[bioinforesearchquestions]

Thanks, I have made changes to the existing post itself.