[Bioc-sig-seq] finding the final nucleotide of trimmed reads

[joseph franklin]

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))

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 <Joern.Toedling at curie.fr> 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
>> 
>> _______________________________________________
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>> 
> 
> 
> 
> -- 
> 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