Hi all, Does anyone know if the shortRead package has functionality to filter out duplicate reads, but only reads with more than n duplicates, to avoid reads stacks caused by PCR-aplification? I can only find srduplicated(), but it doesn't seem to have functionality for specifiying n duplicate reads. Thanks in advance! Regards, JW, Uni. of Copenhagen [[alternative HTML version deleted]]

Hi Johannes -- Johannes Waage wrote: > Hi all, > > Does anyone know if the shortRead package has functionality to filter out > duplicate reads, but only reads with more than n duplicates, to avoid reads > stacks caused by PCR-aplification? I can only find srduplicated(), but it > doesn't seem to have functionality for specifiying n duplicate reads. I don't think there's a built-in function. This f <- function(x, n) { r <- srrank(x) t <- tabulate(r) r %in% which(t >= n) } returns a logical vector indicating that the reads occur >= n times, so aln[!f(sread(aln), 5)] would drop the reads occurring 5 or more times (one might want to think about whether the reads need to map to the same location, too). Martin > > Thanks in advance! > > Regards, > JW, > Uni. of Copenhagen > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793