Question: Detect synthetic miRNA via miRDeep2
gravatar for dinggens
12 months ago by
dinggens0 wrote:


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 and ${sampleid}.fq -e -h -m -l 18 -s ${sampleid}/collapsed.fa ${sampleid}/collapsed.fa -c -p $genome -t $${sampleid}/mapped.arf -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

rna-seq • 195 views
ADD COMMENTlink written 12 months ago by dinggens0

It is simply not possible, you need the precursor sequence.

ADD REPLYlink written 12 months ago by Buffo1.8k
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