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

[Joern Toedling]

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)

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