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. > > _________________________________________________________________ > Show them the way! Add maps and directions to your party invites. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
