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 <mdavy86@gmail.com> 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 <jasreeth@gmail.com>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
>> Bioc-sig-sequencing@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>
>

	[[alternative HTML version deleted]]

