I am trying to identify differentially expressed microRNAs from my NGS data.
I have two conditions (control vs drug) Each condition has three replicates.
I have done the mapping procedure successfully and have done to identify differentially expressed miRNAs..
I have used three protocols.
Interestingly, my result report different results especially for cuffdiff vs edgeR/DeSeq.
The result from edgeR/DeSeq looks very similar.
Under the qvalue < 0.05 threshold,
I have only 2 miRNAs by DESeq and 5 miRNAs by edgeR (luckily, those two miRNAs are overlapped..) Also, when I relax the q value threshold 0.1 , those 5 miRNAs are overlapped in both DESeq and edgeR
However, for Cuffdiff result, I have 27 miRNAs (including Mirlet7d, Mirlet7a-1 etc.. which were not detected by DESeq or edgeR ). And among above 5 identfied DE microRNA (by edgeR/DESeq), only 4 of them are overlapped with 27 miRNAs by Cuffdiff.. Apprently, one of them are not.
So, I am not sure which tool I have to trust. I know different method has different strategry to detect DEG. however, I am nnot sure for my study, which one I have to trust.
Could you please give some comments for this??