Question: Need help in selecting the correct output file from miRDeep2?
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gravatar for bioinforesearchquestions
6 months ago by
United States
bioinforesearchquestions160 wrote:

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?

Commercial Photography

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

Screen_Shot_2018_03_08_at_5_11_20_PM

  • miRNA_expressed.csv Screen_Shot_2018_03_08_at_5_04_37_PM

3) miRNAs_expressed_all_samples_04_03_2018_t_07_26_27.csv

Screen_Shot_2018_03_08_at_5_27_31_PM

4) miRDeep2_output/mirdeep_runs/run_04_03_2018_t_07_26_27/

  • output.mrd

Screen_Shot_2018_03_08_at_5_09_50_PM

mirna rna-seq mirdeep2 mirbase • 283 views
ADD COMMENTlink modified 5 months ago • written 6 months ago by bioinforesearchquestions160

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.

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax55k

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

ADD REPLYlink written 5 months ago by bioinforesearchquestions160
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