Dave,
Before you look for an external solution, I recommend you try the
vcountPattern function in Biostrings. In a training course back in Nov
08 we showed the efficiency of vcountPattern in finding adapter-like reads.
http://bioconductor.org/workshops/2008/SeattleNov08/MatchAlign/MatchAlign.pdf
see pages 7 - 10
As a first approximation, I would guess your code would look something like:
adapter <- DNAString("ACGGATTGTTCAGT")
prefix <- substring(myReads, 1, nchar(adapter))
suffix <- substring(myReads, nchar(myReads) - nchar(adapter) + 1,
nchar(myReads))
whichAdapters <- which(vcountPattern(adapter, prefix, max.mismatch = 1) +
vcountPattern(adapter, suffix, max.mismatch = 1) > 0)
nonAdapterReads <- myReads[- whichAdapters]
adapterReads <- myReads[whichAdapters]
adapterReads
Patrick
Dan Bolser wrote:
2009/1/8 David A.G <[email protected]>:
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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