On Thu, Jul 7, 2011 at 7:14 AM, colin molter colin.molter@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).
Peter