miRDeep2 Support

Question

[VineethVenumadhavan]

Dear Biostars,

Appreciate your support regarding miRNA bioinformatics analysis with miRDeep2. Otherwise please redirect me to an expert / forum to which I can raise these queries. Already emailed developers and a waiting for a response from long. Thanks in advance.

Q1) Which is the best way to perform miRNA analysis

   1)   Find known miRNAs using bowtie homology search with miRBase and take unaligned for novel miRNA prediction using miRDeep2 

    OR

    2)  Find Known and Novel miRNAs using miRDeep2 analysis
            If so,
                    May I know the mirdeep2.pl command mainly to know the order of reference 
                    mirna sequence given for the analysis. Keep in mind that I neither have species Is this anyone from below list

                    A) All animal miRNAs as reference species 
                        miRDeep2.pl reads_collapsed.fa genome.fa reads_collapsed_vs_genome.arf  
                        miRBase_animalmiRNA.fa none animal_miRNA_precursors.fa  -t myspecies 
                        2>report.log

                    B) All animal miRNAs as related species (without giving precursor sequences)
                       miRDeep2.pl reads_collapsed.fa genome.fa reads_collapsed_vs_genome.arf  
                       none miRBase_animalmiRNA.fa none -t myspecies 2>report.log

                    c) Known miRNAs cannot be given, so predict miRNA and later classify using 
                        homology search with mirbase ? 
                       miRDeep2.pl reads_collapsed.fa genome.fa reads_collapsed_vs_genome.arf  
                       none none none -t myspecies 2>report.log

    OR

    3)  Predict all miRNA using miRDeep2 and then perform homology analysis with miRBase 
            to classify known and novel miRNAs.

Q2) I am having an issue with miRDeep2 itself.

   Note: I am running miRDeep2 version 0.1.2.  RNAfold 2.4.17

   After many test analysis in the mirDeep2 results,  

   1)   “estimated probability that the miRNA candidate is a true positive" column have always 
             a value “-“ and    
   2)   “significant randfold p-value" column has always have an output “no”  

   Whether this could be due to an incorrect installation ?