Now that we have processed data from SRP371294 data, we need to make the processed data files available for visualization in IGB.

For this, we will make a sample spreadsheet named SRP371294_sample_sheet.xlsx and then use it as a new input to the script "makeAnnotsXml.py" residing in hotpollen repo "genome-browser-visualization" to enable users to view the data in IGB.

To do:

• Review existing sample sheets in "splicing analysis" repository in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/
• Create a new spreadsheet named SRP371294_sample_sheet.xlsx and fill in the columns using information from Sequence Read Archive records for SRP371294. Use the existing sample spreadsheets as a guide for how best to do this.
• Modify the script "makeAnnotsXml.py" in hotpollen repo "genome-browser-visualization" to include the new spreadsheet. Note that if you have errors in the spreadsheet, the script will likely fail. Also note that you will have modify the script to accommodate a new dataset that not tomato and that does not reside in the same physical location as the others.
• To check the annots.xml file and the resulting visualizations, following the instructions in the "README" file at https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/

To Test:

• Check that every file can be loaded into IGB
• Visualize genes SR45A and SR30 to observe possible splicing differences between sample types.

Other relevant information:

• The physical location of the data files on our data deployment host is: http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/SRP371294/
• Genome version for this data set is A_thaliana_Jun_2009