
Hi Dan, thanks for your comment. Actually I got the idea of using Biostrings from seqanswers, which was thrown in by James W. MacDonald.
see 
http://seqanswers.com/forums/showthread.php?t=780

Apparently Novoalign can also cope with adapters at both ends but only the licensed version will take care of the 5' end adapter.

Any more thoughts?

Cheers,

Dave

> Date: Thu, 8 Jan 2009 16:04:35 +0000
> From: dan.bolser@gmail.com
> To: dasolexa@hotmail.com
> Subject: Re: [Bioc-sig-seq] adapter removal
> CC: bioc-sig-sequencing@r-project.org
> 
> 2009/1/8 David A.G <dasolexa@hotmail.com>:
> >
> > Dear list,
> >
> > I have some experience with Bioconductor but am newbie to this list and to NGS. I am trying to remove some adapters from my solexa s_N_sequence.txt file using Biostrings and ShortRead packages and the vignettes.  I managed to read in the text file and got to save the reads as follows
> >
> > fqpattern <- "s_4_sequence.txt"
> > f4 <- file.path(analysisPath(sp), fqpattern)
> > fq4 <- readFastq(sp, fqpattern)
> > reads <- sread(fq4)  #"reads" contains more than 4 million 34-length fragments
> >
> > Having the following adapter sequence:
> >
> > adapter <- DNAString("ACGGATTGTTCAGT")
> >
> > I tried to mimic the example in the Biostring vignette as follows:
> >
> >
> > myAdapterAligns <- pairwiseAlignment(reads, adapter, type = "overlap")
> >
> > but after more than two hours the process is still running.
> >
> > I am running R 2.8.0 on a 64bit linux machine (Kubuntu 2.6.24) with 4Gb RAM, and I only have some 30Mb free RAM left. I found a thread on adapter removal but does not clear things much to me, since as far as I understood the option mentioned in the thread is not appropriate (quote :(though apparently this is not entirely satisfactory, see the second entry!)).
> >
> > Is this just a memory issue or am I doing something wrong? Shall I leave the process to run for longer?
> >
> > TIA for your help,
> >
> > Dave
> 
> Hi Dave
> 
> I think a stand alone C program may be more appropriate for the task
> you are trying to perform. I'm new to NGS myself, but I believe there
> are many software available to do this. I think the convenience of
> using R natrualy results in a performance hit on some intensive
> algorithms.
> 
> Try asking your question over here:
> 
> http://seqanswers.com/
> 
> 
> or is there a better mailing list?
> 
> Cheers,
> 
> Dan.
> 
> >
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