Hello Jianguang,
Please see "Basic Protocol 2: Loading Data and Understanding Datatypes" in this tutorial/publication:
http://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
The third dataset is the RefSeq genes dataset extracted from the UCSC Table browser. You could use this version or pull the latest (it is updated 6 days a week).
Alternatively, to take full advantage of the options in CuffDiff, you could use the iGenomes version of a reference GTF as explained in the updated RNA-seq protocol:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
The exercise has GTF for a single chrom, but the full dataset is in Shared Data Libraries -> iGenomes -> mm9 -> genes.gtf (https://main.g2.bx.psu.edu/library)
Reviewing the CuffDiff documentation will explain why the iGenomes dataset is preferred, but in short is because of the presence of additional attributes used by the tool to calculate differential expression values. This may or may not be part of your analysis plan, the RNA-seq tutorial should help you decide, as well as the CuffLinks "Getting Started -> Common uses" sample analysis at: http://cufflinks.cbcb.umd.edu/tutorial.html
Hopefully this offers you some choices,
On 8/14/12 9:11 AM, Du, Jianguang wrote:
Dear All,
I am going to search the alternative splicing events bentween datasets. I am not sure about the settings of mouse reference genome (mm9) when I upload it from UCSC Main.
Would you please tell me the settings for
group:
Track:
Table:
Output format:
Thanks.
Jianguang
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