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