Question: Detect synthetic miRNA via miRDeep2
0
gravatar for dinggens
12 months ago by
dinggens0
Germany
dinggens0 wrote:

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

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1594 users visited in the last hour