Howdy, On Thu, Aug 26, 2010 at 9:29 AM, Joern Toedling <[email protected]> wrote: > Hi, > > have a look at the "shift" argument of the function consensusMatrix from > Biostrings. > > This code example should correspond to your question. Three nucleotide strings > are aligned at their last position and the sequence composition is obtained: > > A <- DNAStringSet(c("ACAT", "CAT", "AGGGCGT")) > maxlen <- max(nchar(A)) > consensusMatrix(A, shift=maxlen-nchar(A), baseOnly=TRUE)
Alternatively: R> last <- subseq(A, start=width(A), width=1) R> consensusMatrix(last) -steve > I tested this with Biostrings_2.17.29, but I guess that it works with the > current release version, too. > > Regards, > Joern > > > On Thu, 26 Aug 2010 07:35:01 -0500, joseph franklin wrote >> Hi, >> >> I've been trimming adapters from reads using trimLRPatterns. The >> resulting, trimmed set contains a heterogenous mix of widths: from >> ~18-35 nt. Can anyone guide me toward an elegant way to find the >> nucleotide composition of the final (right-most) cycle for each of >> the trimmed reads? >> >> Many thanks, >> Joe Franklin > > --- > Joern Toedling > Institut Curie -- U900 > 26 rue d'Ulm, 75005 Paris, FRANCE > Tel. +33 (0)156246927 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
