Dear Simon, I hope you don't mind that I am copying the Bioconductor list - your question may be relevant to others as well. The reason for extending the mature miRNA coordinates depending on their strand lies in the way QuasR's qCount determines if an alignment overlaps with a query region: By default, qCount counts alignments if the 5'-end base is contained in the query region (see ?qCount, selectReadPosition="start"). The example in the vignette (section 6.3.3) therefore constructs a query region for each mature miRNA around its 5'-end, which corresponds to start(matureMirs) for plus-strand miRNAs, and to end(matureMirs) for minus-strand miRNAs. The resulting query region is 7 nucleotides long and allows for some variability in the processing of mature miRNAs, yet it is narrow enough to not also count reads that are unlikely to be Dicer-processed mature miRNAs. You are right that in the vignette, only mature miRNAs are quantified. This is just an illustration; you could also create query regions corresponding to the pre-miRNAs to also include reads that stem from the precursor. Michael On 19.05.2014 18:12, Simon de Bernard wrote: > Dear Michael, > > I was looking at the miRNA part of your vignette for QuasR (http://m aster.bioconductor.org/packages/release/bioc/vignettes/QuasR/inst/doc/ QuasR.pdf). > > When you extend the the start and end positions (page 34), should you really test for the strand? > Shouldn't it simply be: > > start(matureMirsExtended) <- start(matureMirs) - 3 > end(matureMirsExtended) <- end(matureMirs) + 3 > > Also, in your exemple, you do not extend the preMirs. Is this intentional? > > Thanking you in advance, > > Best regards, > > Simon. >