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rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data
GNU General Public License v3.0
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One precursor have two locations of mature miRNA sequence #111

Closed Yuzhang0102 closed 1 year ago

Yuzhang0102 commented 1 year ago

Hi, I firstly merged and collapsed my all fastq data of all samples to predict novel miRNAs by miRDeep2.pl. Then I used the output precursor and mature fasta to run quantifier.pl for each sample. But I got two reads counts of some miRNA in the results. quantifier.pl -p novel_pres_07_04_2023_t_15_26_33_score-50_to_na.fa -m novel_mature_07_04_2023_t_15_26_33_score-50_to_na.fa -r sample1.fa -d I checked these miRNAs found that the precursor have two locations of mature miRNA sequence, like this: image But the mature miRNA structure is this: image So my questions are

  1. Do quantifier.pl and miRDeep2.ple have different mapping strategy? The reads mapping to the precursor are unique mapped, for quantifier.pl how to decide the read map to which location?
  2. The second mature miRNA is the miRNA predicted by mirdeep2.pl, but its counts are less than the first miRNA, why?
  3. Can this sRNA still be a positive miRNA?
mschilli87 commented 1 year ago

IIRC, miRDeep2.pl calls (potentially novel) miRNA(-precursor)s from reads mapped to the genome, whereas quantifier.pl maps reads to (annotated) miRNAs (trading specificity for sensitivity). I hope this answers your first question. Regarding your second and third question, I am not sure I get what you are asking. Maybe @Drmirdeep can provide a better answer.

Drmirdeep commented 1 year ago

Please have a look at the publication and the tools help regarding the options used by quantifier.pl and mirdeep2.pl

Yuzhang0102 commented 1 year ago

Thanks for your replies! I have looked at the options of quantifier.pl many times, but I don't know how to avoid this condition, or it can't be avoid?