Hello,
I have a question regarding the detection of synthetic miRNA. So far I have been using miRDeep2 for biological data and it worked fine. Now, synthetic miRNA are not detected/counted, although I adapted the input files accordingly by adding the synthetic miRNA to the reference files ($genome, $mature) for mapper.pl and quantifier.pl:
mapper.pl ${sampleid}.fq -e -h -m -l 18 -s ${sampleid}/collapsed.fa
mapper.pl ${sampleid}/collapsed.fa -c -p $genome -t $${sampleid}/mapped.arf
quantifier.pl -p $hairpin -m $mature -r ${sampleid}/collapsed.fa -t $spshort
According to the miRDeep developers, also the precursors ($hairpin) have to be adapted. Can anyone tell me how to do this, or is it possible to use miRDeep2 without providing precursors?
Many thanks in advance
It is simply not possible, you need the precursor sequence.