On Thu, Jul 7, 2011 at 7:14 AM, colin molter <colin.mol...@gmail.com> wrote:
> Hi all,
> i am trying to use a local instance of my galaxy to pre-format data stored
> at sra-ncbi.
> Does anyone has a working pipeline that (s)he could share.
> Here is the pipeline I am using, with some questions.
> 1/ download sra files to my server.
> 2/ transform them in fastq using the sra toolbox.
> 3/ upload them in galaxy, by using the 'add to data library'
> 4/ use the fastq groomer to enable to use the fast q in galaxy.
> Note: i guess that the data at sra are already in the fastq sanger format.
> So it could be nice to be able to skip that point (it took 10 hours to groom
> a fastq of 25Gb).

Just upload load them and set the file format to fastqsanger
(either when you upload, or afterwards via the pencil icon
to edit the attributes - this is fast as it doesn't change the file).

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