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RNA-Seq Module 3 . User input

RNA-Seq module 3 tutorial of April 10th, 2012 has been postponed.

New tutorial date:
    Wednesday May 23rd, 10-Noon;   Room 402 Walter Library

Outline Draft
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.