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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