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!