I have used mirdeep2 to identify novel miRNAs, I have 18 samples and a number of common mature sequences. What I have realised the in some sample the common precursor_coordinate differs by 1-3 nucleotides.
I wanted to do a differential analysis between the samples, As mirdeep2 provides different provisional ID, its not possible to do differential analysis on that result. so the idea was to insert the coordinates into the GTF file and count the know and novel miRNA genes using HTseq. Now due to the variation in the coordinates of the miRNA it is difficult to put them in the GTF. At this moment I am not sure how to deal with this issue. I will appreciate any suggestions.
Thanks for your help