On 08/26/2010 03:22 PM, joseph franklin wrote: > Many thanks for all the advice. For the record, to get subseq() to work I > had to flatten the trimmed reads to a character object: > > trimmedseq<-as.character(sread(trimmed))
Hi Joe --that shouldn't be necessary, just subseq(sread(trimmed), start=width(trimmed), width=1) or one of the other suggestions. Or what am I missing? Martin > > There may be a better way to accomplish that. > > Then this works great: > > last <- subseq(trimmedseq, start=width(trimmedseq), width=1) > consensusMatrix(last, as.prob=TRUE) > > -joe > > > On 26 Aug 2010, at 9:26, Steve Lianoglou wrote: > >> 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 -- 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
