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Event Details
February 13th, 2013 8:30 AM - 3:45 PM
Farrell Learning and Teaching Center
Rooms 404 A&B
United States

This will be a hands-on workshop using JMP Genomics, version 6.0. Data will be provided. Please bring your own laptop with JMP Genomics 6.0 installed. Download JMP Genomics 6.0.

Please download and review the PDFs at the links provided below prior to the training. The complete set can be found here.

If you have any questions please contact Marcy Vana at Becker Library at or 362-2796.

Session I: Important Features of JMP Genomics 6.0 - Morning (8:30-11:30)

1. JMP Genomics 6.0: Software Overview and New Features (8:30-9:30 with 5 min break)

Navigating in JMP Genomics

Basic Processes

Output Files

Tips and Tricks


2. Importing Genetics Data into JMP Genomics 6.0 (9:30-10:00)

Affymetrix and/or Illumina Data

Text/PLINK Files

3. Import and Analysis of Next-Generation Sequencing Data with JMP Genomics 6.0 (10:00-11:30)

Preferred File Formats

BAM and TXT File Importing

Filtering, Normalization

Quality Control

Modeling and Results


Lunch Break (11:30-12:30)

Session II: Advanced Genetic Analysis with JMP Genomics 6.0 - Afternoon (12:30-3:45)

4. Review of File Formats and Ordering (12:30-12:45)

Covered in depth in:

5. Recode Genotypes, Relationship Matrix, PCA for Population Stratification (12:45-1:45 with 5 min break)       

6. Annotation Analysis, KEGG Pathways (Aldi Kraja, 1:45-2:15 with 5 min break)

7. Multiple SNP-Trait Association, Pleiotropic Association and Rare-Variant Analysis (2:15-3:45)

Refer to Advanced Genetic Analysis Document from the link in (5)

8. Social (3:45-4:00)

Time for JMP Genomics team to respond to any other questions after the workshop