Hello Jianguang, This depends on how the library prep was done (which protocol was followed). Some preserve strand and some do not. If you did not prepare the data yourself, then the data source should be able to provide you with this information. Hopefully this helps, Jen Galaxy team On 4/15/13 10:42 AM, Du, Jianguang wrote:

Hi All,

I have a very basic question about parameters for running TopHat.

I have datasets of single-end reads. These datasets were generated with Illumina Genome Analyzer IIx. Which "Library Type" should I choose to run Tophat?

Thanks.

Best,

Jianguang

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