I am new to R and don't quiet understand this correctly. When I tried ?writeFastq , nothing is displayed. Is there is any other way to export the trimmed reads? I am using this workflow: http://www.bioconductor.org/help/workflows/high-throughput-sequencing/
Thanks! On Mon, Aug 16, 2010 at 5:50 PM, Marcus Davy <[email protected]> wrote: > One option is to try writeFastq to fastq format, I believe it was working > on recently and is fast. > > exptPath <- system.file("extdata", package = "ShortRead") > sp <- SolexaPath(exptPath) > fqpattern <- "s_1_sequence.txt" > fl <- file.path(analysisPath(sp), fqpattern) > fq <- readFastq(sp, fqpattern) > > tf <- tempfile(tmpdir="/tmp") > > writeFastq(fq, tf) > > > Marcus > > > On Tue, Aug 17, 2010 at 10:42 AM, JASREET HUNDAL <[email protected]>wrote: > >> Has anyone worked with trimLRPatterns function in the ShortRead library >> for >> adaptor trimming? >> What is the best way to export the trimmed reads in a fasta/fastq/text >> file? >> I have a large 5,000,000 line fastq file with 50bp reads as input. >> I have tried write.table as well as writeFASTA but nothing seems to be >> working. >> Hence, I would appreciate if somebody could help me out as I am novice in >> the world of R/Bioconductor. >> >> Thanks >> -Jess >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
