Hello Mark,

The first item to double check is the data type. Make sure that is assigned correctly, as described here:
http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

Please let us know if this doesn't resolve the issue,

Jen
Galaxy team

On 11/16/13 5:09 PM, mark.r...@syngenta.com wrote:

Hi All

I'm trying to use bowtie2 in Galaxy but though I have uploaded a valid pair of fastq files, Galaxy seems to recognize only one of the and places it in both inputs for paired end reads without any other options in the drop down menus.

Thanks for your help

Mark



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