BTEP Workshop on RNA-Seq Data Analysis (2-day)
This 2-day workshop, which includes both lecture and hands-on components, will cover the fundamentals of and best practices for RNA-Seq Data Analysis. Learn everything from experimental design and sample prep requirements, to alignment, quantification, generation of differentially expressed genes, and understanding the results after completion of analysis. There will be presentations and training on using both open source (CCBR RNA-Seq Pipeline) and commercial (Partek Flow) software.
NOTE: This is a BYOC (Bring your own laptop Computer) class. Government issued or personal computers are permitted. We will be able to supply a very limited set of computers, so if you want to take the class but cannot bring your own computer please indicate such in the Comment section on the registration form.
For CCR staff located outside of the Bethesda campus, the talks will be webcast for your convenience. Please register for the webinar here: https://attendee.gotowebinar.com/register/469987726031396353
Monday, March 20 – Morning Session
Alignment – aligners, transcriptome vs genome, non-aligners
Expression quantitation, FPKM, counts, Junctions reads
Normalization (different methods)
Differential Expression gene/transcriptome lists
- Multi-QC results
- Differentially Expressed Genes
- Isoform Expression (high-level review)
- Viewers – Manual validation (IGV)
- Principal Component Analysis (PCA)
- Clustering – Different methods
- Pathway Enrichment (GSEA)
6. Final, brief hands-on session for ONLY those who fulfill the following requirements:
- Already have an existing Biowulf/Helix Account
- Basic working knowledge of command line on Terminal
- Functional XQuartz application (https://www.xquartz.org/releases/XQuartz-2.7.11.html)
This is applicable for only this last session on Day 1. Not necessary for other sessions on Day 1 or Day 2.
Day 2 – Tuesday, March 21
LUNCH BREAK 12:30 – 1:00 pm
· Partek Flow
• Getting set up on NIH Helix server
• Importing data
• Performing QA/AC
• Gene/transcript abundance estimation
• Differential expression detection
• Go Enrichment analysis
• Visualization (PCA, dotplot, volcano plot, chromosome view, hierarchical clustering etc.)
• Microarray analysis and integration with RNA-seq data.
· Partek Genomics Suite
• Importing Partek Flow project and text file format
• Visualization (PCA, dot plot, heatmap etc.)
• Pathway analysis
• Integration of genomic data.