I am using Mirdeep2 to identify miRNA in my organism (none model organism) which has no previously identified micro_RNAs. My organism is genetically close to Drosophila melanogaster. My understanding if that with mirdeep2, one can use closely related organism mature miRNAs to identify the micro-RNA of the other. Since this is the case with my organism, I used Drosophila mature microRNAs sequences to get what is in my organism. I do get results, but my problem is that the Randfold p-value for all the predicted miRNAs are not significant ('no'), even for majority which have perfect match homology. My script is:
miRDeep2.pl A_collapsed.fa A.fasta A_collapsed_vs_genome.arf none miRBase_dme_v14.fa none 2>A_report.log
Randfold results for this is 'no' When I run test for mirdeep2 for organism with some previously predicted miRNA (script below), I get normal results with Randfold p-value being significant ('yes') for most and some 'no'. This means my installation is okay.
miRDeep2.pl A_collapsed.fa A.fasta A_collapsed_vs_genome.arf A.miRNA.fasta miRBase_dme_v14.fa miRBase_dme_v14hairpin.fa 2>A_report.log
I am wondering if anyone has experienced a similar situation as what I have described in the first part for none model organism without previously identified miRNA and how you went about it. Or anyone who knows how to solve this issue, please help. Thanks
