<p>Hi all.I am dealing with some miRNA data sequenced by illumina Htseq 2000.And I confuse the result of the mirdeep2 software.
First is the result of the quantifier.pl.In the miRNAs_expressed_all_samples_time.csv has entries show below.</p>

<pre><code>hsa-miR-1       549.00  hsa-mir-1-1     549.00  420.00  129.00  19.07   23.63
hsa-miR-1       564.00  hsa-mir-1-2     564.00  432.00  132.00  19.62   24.18
</code></pre>

<p>The same miRNA with different precursor.I am not sure how to deal with these when I try to use the R package DEGseq to detect
DE miRNA.Treat them as two different entries or just plus them if  these entries have no intersection.</p>

<p>Second,the result of <code>less output.mrd |grep '&gt;'|wc -l</code> is 1789.I think it hsa 1789 precursors,and the result.csv file just have 785 novel and known miRNAs, I don't know how to explain the different between these two numbers.
Your reply will be appreciated.
Cheers.</p>

<p>Different miRNA precursors can produce the same mature form.</p>

<p>In such cases, it depends on the type of  your downstream analysis.</p>

<p>If you are interested in precursor expression then these two (and all others that fall in this category) should be considered as separate features.</p>

<p>If your analysis focuses on mature miRNAs (for target identification, etc) then these two matures should be considered as one, since they have the same mature sequence (same targets, etc).</p>

<p>Depending on your miRDeep 2 settings (if you divide multimaps or not), you can just add the expression of those two mature miRNAs into one, or keep one with just their average.</p>

<p>Cheers,</p>

<p>IV</p>
