[Bioc-sig-seq] About trimming adaptor of Solexa short reads

[Thomas Girke]

I would use the trimLRPatterns function in Biostrings that Patrick Aboyoun 
implemented recently (available in BioC 2.4). The function does exactly what 
is needed for trimming adaptors in short read data sets, e.g. small RNA 
experiments. In addition, it runs really fast. 

Here is a short example from one of our recent workshops on short read analysis
with BioC:
http://htseq.ucr.edu/HT_BioC_Manual#TrimmingofFlankingSequences


Thomas


On Thu, Apr 30, 2009 at 11:02:03AM -0400, James W. MacDonald wrote:
> 
> 
> Dan Bolser wrote:
> >2009/4/27 James W. MacDonald <jmacdon at med.umich.edu>:
> >>There is some older information from BioC2008 here (starting on page 12):
> >>
> >>http://www.bioconductor.org/workshops/2008/BioC2008/labs/PairwiseSequenceAlignments/Alignments.pdf
> >>
> >>Or you could search the Bioc-sig-seq listserv for newer information:
> >>
> >>http://www.google.com/search?hl=en&as_q=adapter&as_epq=&as_oq=&as_eq=&num=10&lr=&as_filetype=&ft=i&as_sitesearch=https%3A%2F%2Fstat.ethz.ch%2Fpipermail%2Fbioc-sig-sequencing%2F&as_qdr=all&as_rights=&as_occt=any&cr=&as_nlo=&as_nhi=&safe=images
> >
> >Is there a wiki where this info gets logged?
> 
> Unfortunately, no (or fortunately, if you are the person charged with 
> updating the wiki). We have dabbled a bit with using a wiki to track 
> information or certain long-running discussions, but it's like having a 
> microwave at work - most people want to use it, but nobody has the time 
> or inclination to keep it clean.
> 
> Fortunately there are many people who subscribe to the various BioC 
> lists who are more than helpful, and our friend google is really good at 
> finding their responses, given the correct search string. So we rely on 
> the list archives as the primary store of information rather than a wiki.
> 
> Best,
> 
> Jim
> 
> >
> >
> >>Best,
> >>
> >>Jim
> >>
> >>
> >>Xiang Xu wrote:
> >>>Hello all,
> >>>
> >>>Is there someone can show me some software or tools for trimming the
> >>>adaptors of Solexa short reads? Do you have any protocol for analysis
> >>>sequencing data of gene expression and small RNA?
> >>>
> >>>Thanks in advance.
> >>>
> >>>Regards,
> >>>
> >>>Xiang Xu
> >>>
> >>>       [[alternative HTML version deleted]]
> >>>
> >>>_______________________________________________
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> >>>Bioc-sig-sequencing at r-project.org
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> >>--
> >>James W. MacDonald, M.S.
> >>Biostatistician
> >>Douglas Lab
> >>University of Michigan
> >>Department of Human Genetics
> >>5912 Buhl
> >>1241 E. Catherine St.
> >>Ann Arbor MI 48109-5618
> >>734-615-7826
> >>
> >>_______________________________________________
> >>Bioc-sig-sequencing mailing list
> >>Bioc-sig-sequencing at r-project.org
> >>https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >>
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> 
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