[Bioc-sig-seq] adapter removal

[Dan Bolser]

2009/1/8 David A.G <dasolexa at 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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