Maya,

Many tools require that fastq files specify that they are of sanger quality 
score.  Specifically, "Map with BWA for Illumina", etc.  If you click the 
pencil icon ("Edit Attributes") on your uploaded dataset and change the data 
type from 'fastq' to 'fastqsanger', you should be able to run your tools.

Thanks, and let me know if you have any other issues.

Dannon

On Nov 10, 2011, at 5:20 PM, Maya Kasowski wrote:

> Hello,
> 
> I uploaded a couple fastq files to Galaxy (Illumina GA2X sequencer).
> The files uploaded successfully and are green in the history section.
> However, neither file is visible in the drop down menus for any of the
> tools. I'd appreciate your help with this.
> 
> Thank you,
> Maya
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___________________________________________________________
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