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

[Steve Lianoglou]

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