
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

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