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
