Question: Duplicate miRNAs with different read counts in miRDeep2
gravatar for PAn
4.2 years ago by
United States
PAn20 wrote:


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!

ADD COMMENTlink modified 4.2 years ago by benformatics2.0k • written 4.2 years ago by PAn20

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!

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Mike Lafferty0
gravatar for benformatics
4.2 years ago by
ETH Zurich
benformatics2.0k wrote:

I believe this was answered previously:

Mirdeep2 Quantifier Module Output

ADD COMMENTlink written 4.2 years ago by benformatics2.0k
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