Duplicate miRNAs with different read counts in miRDeep2

Question

[PAn]

Hello,

I am using miRDeep2 to calculate the read counts for a sequenced Mouse sample. I am using mature miRNAs and hairpin miRNAs from mirbase to calculate the read counts. I would expect unique miRNAs in the miRDeep2 result file - miRNAs_expressed_all_samples_sample.csv, but it gives different read counts for same mature miRNA and precursor combination.

mmu-miR-466i-5p 136.00  mmu-mir-466q    136.00  136.00  10.25
mmu-miR-466i-5p 152.00  mmu-mir-466q    152.00  152.00  11.46
mmu-miR-466i-5p 187.00  mmu-mir-466q    187.00  187.00  14.10
mmu-miR-466i-5p 156.00  mmu-mir-466q    156.00  156.00  11.76

There are few more miRNAs with similar results in the csv file. Has anyone else seen these kind of duplicate miRNAs with different read counts as well? I did see a nature paper addressing this issue while comparing miRDeep2 to mirPRO, but it will be good to know if anyone knows on how to resolve it. My aim is to run DESeq using these read counts, but since there are duplicate miRNA entries, I cannot use the miRDeep read counts as miRNAs are not unique. Thanks!

[Mike Lafferty]

Did you ever find an answer to this question? I'm having the same problem with miRDeep2 (and the below answer is not the same question!). Are you still using miRDeep2 or did you switch to mirPRO or something else? Thanks!

Answer 1

[benformatics]

I believe this was answered previously:

Mirdeep2 Quantifier Module Output