Genomics, RNA-Seq, Assembly, Annotation, Variation, Quality Control, ChIP-Seq
- Ben Busby, Sijung Yun
This is the syllabus for a popular NGS workshop that heavily uses Galaxy as a teaching tool. If there seems to be interest, we intend to add specific tutorials.
Contact: Ben Busby <ben DOT busby AT gmail DOT com>
Syllabus for July, 2014 Next Generation Sequencing Course, Biotrac Program
Tuesday, July 8th: DNA-seq
- 9:00-9:45: Course Introduction, Administrative Announcements and Probability with Goats (Mark Nardone, Sijung Yun, Ben Busby)
9:45-11:30: Introduction to Next Generation Sequencing (NGS) including library construction & details on Illumina’s technology (Ben Busby, Heekyong Bae, Sijung Yun)
- 11:30-12:00: Galaxy for NGS data analysis (Ben Busby -- slides courtesy of Matt Shirley)
- 12:00-1:00: Lunch -- 12:30 - Using Galaxy on Helix! (David Hoover)
- 1:00 - 3:30: DNA-seq and variation calling with Galaxy (Sijung Yun)
- 3:30 - 4:00: Working with .vcf files: Variation Reporter and Variation Viewer (Ben Busby)
- 4:00 - 5:00: Medgen/GTR/Clinvar (Adriana Malhiero)
Wednesday, July 9th: RNA-seq and CHIP-seq
- 9:00 - 10:30: Finishing up DNA-seq lab
- 10:40 - 11:20: Introduction to Advanced Techniques, Variant callers, 1,000 Genomes and the SRA toolkit (Ben Busby)
- 11:20 - 11:45: Epigenomics (Ben Busby)
- 11:45 - 12:45: Lunch
- 12:45 - 1:45: Special Lecture! -- Considerations for metagenomic datasets (Julia Oh)
- 1:45 - 2:30: RNA-seq and CHIP-seq with Galaxy (Sijung Yun, Ben Busby)
2:30 - 5:00: Continue RNA-seq and CHIP-seq with Galaxy & Lab (Sijung Yun, Ben Busby)
Thursday, July 10th: -- Command line analysis:
- 9:00 - 9:30: Introduction to Biowulf (Susan Chacko)
- 9:30 - 9:45: Aggregate probability exercise and pop quiz about reference genomes
- 9:45 - 11:15: Introduction to Linux
- Basic commands (Sijung Yun, 30 min) ALTERNATE SESSION FOR LINUX-SAVVY STUDENTS -- BUILDING RNA-seq pipelines
- Beyond basic commands
- Case Study: Moving files to run the tuxedo package.
- 11:30 - 12:30: sed and awk (Ben Busby)
- 12:30 - 1:30: Lunch (metadata normalization discussion)
- 1:30 - 2:00: Introduction to Linux Applications and Cloud Computing (Ben Busby)
- 2:00 - 4:00: DNA-seq in Command Line (Sijung Yun)
- 4:00 - 5:00: Downstream Analysis of RNA-seq and CHIP-seq data (Suntae Kim)
Friday, July 11th: Applications
- 9:00 - 9:10: Aunt Linda Combinatorial Probability Game
- 9:10 - 9:40: Variation Resources, Expression and Epigenomic Data Acquisition at NCBI. Genomic data compression. SRA format, and an introduction to the SRA toolkit.
- 9:30 - 10:15: Building pipelines, de novo assembly, mapping and assembling with paired-end sequences, hybrid mapping (Ben Busby)
- 10:45 - 12:30: BLAST and other basic bioinformatic tools, the SRA toolkit, personalized medicine (Ben Busby)
- 12:30 - 1:30: Lunch
- 1:30 - 3:00: RNA-seq with Tuxedo package in Command Line (Sijung Yun)
- 3:00 - 3:15 BREAK
- 3:15 - 4:30: Lab for downstream analysis of NGS data with command line BLAST (Wayne Matten)
4:30 - 5:00: Follow up and feedback on labs. Discussion of individual projects. Q&A with instructors. Follow up on RNA-seq: tips, tricks and questions (Ben Busby, Sijung Yun)"
For the Galaxy component, we work through an Amazon cloud deployment of Galaxy, with the SRA_toolkit installed from the main toolshed. I can post the AMI for the command line component upon request.
We use very small c elegans datasets. This allows us to host many students in parallel. Posted upon request.
Ben Busby <ben DOT busby AT gmail DOT com>