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Question: Whixh Setting Should Be Used To Upload Mouse Reference Genome?
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gravatar for Du, Jianguang
6.3 years ago by
Du, Jianguang • 380
Du, Jianguang • 380 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 1) group: 2) Track: 3) Table: 4) Output format: Thanks. Jianguang
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modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by Du, Jianguang • 380
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gravatar for Jennifer Hillman Jackson
6.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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, -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k
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