Entering edit mode
3.7 years ago
VineethVenumadhavan
▴
50
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 ?
