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Hello,
I am facing a challenge with the output of mirdeep2 for non model organism with not previously identified microRNAs. Since my organism of interest has no previously identified microRNAs, I understand that I can use mature microRNA of genetically closer organism to mine. However, when I run this, all the microRNAs identified have a Randfold p-value 'no' suggesting that all those microRNAs predicted in my organism are not real. I think there is problem somewhere which I cannot point at. My script for running this is:
mapper.pl A.fastq -e -h -i -j -l 18 -r 5 -m -p ./A_index/Amm -s A_collapsed.fa -t A-reads_vs_refdb.arf -v -o 16
then
miRDeep2.pl A_collapsed.fa A.fasta A_collapsed_vs_genome.arf none miRBase_dme_v14.fa none 2>A_report.log
Any suggestion here will be appreciated.
NOTE: I had run another analysis on a different organism with some microRNAs already identified, and the results were fine. Am not sure what is going on in this new one. Any help please.
Erick
I am facing a challenge with the output of mirdeep2 for non model organism with not previously identified microRNAs. Since my organism of interest has no previously identified microRNAs, I understand that I can use mature microRNA of genetically closer organism to mine. However, when I run this, all the microRNAs identified have a Randfold p-value 'no' suggesting that all those microRNAs predicted in my organism are not real. I think there is problem somewhere which I cannot point at. My script for running this is:
mapper.pl A.fastq -e -h -i -j -l 18 -r 5 -m -p ./A_index/Amm -s A_collapsed.fa -t A-reads_vs_refdb.arf -v -o 16
then
miRDeep2.pl A_collapsed.fa A.fasta A_collapsed_vs_genome.arf none miRBase_dme_v14.fa none 2>A_report.log
Any suggestion here will be appreciated.
NOTE: I had run another analysis on a different organism with some microRNAs already identified, and the results were fine. Am not sure what is going on in this new one. Any help please.
Erick