[Bioc-sig-seq] trimLRPatterns - adaptor trimming

[Martin Morgan]

JASREET HUNDAL <jasreeth at gmail.com> writes:

> 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/

Hi Jess --

what is the output of

  > sessionInfo()

? Hopefully you're using R 2.11.0 or more recent, and ShortRead 1.6.0 or
better. If not, update your R or (if your R is current but not
ShortRead) installed packages as outlined at

  http://bioconductor.org/install/index.html#update-bioconductor-packages

In the workflow you mention, it should be as easy as

  writeFastq(trimmed, "/path/to/file")

It is a little more convoluted for fasta output

  fa <- sread(trimmed)
  names(fa) <- id(trimmed)
  write.XStringSet(fa, "/path/to/file")

It can help to try to convey what you mean by  'nothing seems to be
working' by copying and pasting a part of your R session into your
email,  especially if the snippet is reproducible (e.g., previously
running example(readFastq), and using the 'rfq' object that is created
as the data you're trying to write to a file). Also, if things just seem
to hang, then maybe you could confirm that you have the 'right idea' by
trying to write a subset of the data, e.g., writeFastq(trimmed[1:10]

Martin

> Thanks!
>
>
> On Mon, Aug 16, 2010 at 5:50 PM, Marcus Davy <mdavy86 at 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 at 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]]
>>>
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>>>
>>
>>
>
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>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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