[BioC] ShortRead information

[Martin Morgan]

On 05/27/2010 06:00 AM, Jennifer Dupiot wrote:
> Dear all,
> 
> I am new to bioconductor and little experienced in R.
> I work on illumina data, and would like to analyse Run with ShortRead.
> I have questions about using ShortRead :
>    * Is it  necessary  to  use  whole illumina run folder to do quality
> analysis ? or only fastq files could be sufficients ?

fastq is sufficien
>    * I tried to run following command :
>>
> sp<-SolexaPath("/media/data/CSE/Delivery_2010.02.26/17.2_FlowCell61BWR_75ntX75nt_3.7GB/",analysisPath="/media/data/CSE/Delivery_2010.02.26/17.2_FlowCell61BWR_75ntX75nt_3.7GB/17.2_6_1_sequence.fastq/")
> 
>> ap<-analysisPath (sp)
>> reads<-readFastq(ap,"fastq")
> 
> and it returns :
> "Erreur dans .local(dirPath, pattern, ...) :
>  cannot open file
> /media/data/CSE/Delivery_2010.02.26/17.2_FlowCell61BWR_75ntX75nt_3.7GB/17.2_6_1_sequence.fastq//s_6_1_sequence.fastq"
> 
> 
> Do I do something wrong ?
> Do I miss something ?
> Could you give me some clues on this ?
> 
> For information, computer configuration is :
>    ubuntu 9.10
>    R 2.9.2
>    ShortRead 1.2.1

Hi Jennifer

Update to R-2.11, and reinstall or update Bioconductor packages

  http://bioconductor.org/docs/install/

Use the command sessionInfo() as a more reliable  way to report your
system configuration.

If your fastq files are in a directory "/some/path" then you might
confirm that the files are present where you think they are

  ## Only fastq files in diretory? use
  list.files("/some/path")
  ## otherwise, specify an appropriate regular expression
  list.files("/some/path", "fastq$")
  ## ok, files look good
  rfq = readFastq("/some/path", "fastq$")

if this still fails please provide the result the corresponding
list.files command, and the first few lines of the file that is not
begin read.

HOpe that helps.

Martin

> 
> Thanks for your help.
> Regards,
> 
> Jennifer
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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