On 08/26/2010 04:58 PM, Martin Morgan wrote:
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?
Or alternatively:
subseq(sread(trimmed), start=-1)
Cheers,
H.
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
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Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246927
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| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
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E-mail: [email protected]
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