RNA-Seq module 3 tutorial of April 10th, 2012 has been postponed.
New tutorial date:
Wednesday May 23rd, 10-Noon; Room 402 Walter Library
1. Key definitions, parameters and concepts in RNA Seq ( review of tutorial module 2)
2. Visualization and exploration of results
Purpose: Critical evaluation of analytical result output
- Visual inspection: Based on biological knowledge are specific known genes behaving the way one would expect?
Tool: IGV - Integrated Genome viewer to display BAM alignment files
- Analytical inspection: Variation within a group and across groups; clustering.
Method: PCA - Principal Component Analysis; MDS - multidimensional scaling plot
Reviewing mapping statistics
How to accomplish this with the tools available through MSI
3. Insuring analytical consistency - Avoiding TopHat pitfalls
Purpose: Running TopHat in discovery mode.
How to achieve consistency to support comparative analysis
We invite you to comment on this outline OR to give us input by submitting example of questions you would like to see covered in a trouble-shooting tutorial on RNA-Seq data analysis.
This venue can also be used to suggest other tutorial topic.