index.md

Next-Gen Sequence Analysis Workshop (2017)

These are the schedule and classroom materials for the ANGUS workshop at UC Davis, which will run from June 26th to July 8th, 2017.

This workshop runs under a Code of Conduct. Please respect it and be excellent to each other!

Twitter hash tag: #ngs2017

The main workshop materials

Monday, Day 1: Introduction

7:30pm - 9pm, Valley Hall.

Introductions!

Booting a cloud computer from Jetstream!

Running BLAST at the command line

Assessment.

Student 30-second introductions.

Tuesday, Day 2: Command line.

9am lecture: C. Titus Brown, UC Davis - "On Biology and Data Analysis."

Morning: 10:15am.

• Running large scale BLASTs and output.

Afternoon: 1:15pm - 3pm.

• Visualizing BLAST score distributions in RStudio
• Review and explore: Command line UNIX, and R/RStudio

Evening: 7pm-8:30: student presentations and questions! Ice cream social.

Wednesday, Day 3: Mapping, aligning, and sequence files.

9am lecture: Melissa Wilson Sayres, Arizona State University - "Sex-biased genome evolution"

Morning and afternoon: 10:15am-4pm.

• Quality trimming your reads.
• Mapping and samtools and variant calling.
• High Throughput sequencing. What could go wrong?

(Evening: free time - Wed Farmers' market!)

Thursday, Day 4: Introduction to counting and differential expression.

9am lecture: Chris Hamm, Monsanto - Why are there so many butterflies?

Morning: 10:15am-noon

• Introduction to R and Data Analysis

Afternoon and evening: 1:15pm-3pm, 7-8:30.

• Short reads and counting for variant calling and differential expression

Friday, Day 5: Reference independent analyses: assembly

9am lecture: Adrienne Roeder, Cornell - Reaching biological conclusions from RNA-seq: the good, the bad, and the ugly

Morning: 10:15am-noon.

• Microbial genome assembly

Afternoon: 1-3pm.

• Prokka genome annotation

Evening: (also running on Saturday afternoon; you only need to come to one.)

• Introduction to automation.

Saturday, Day 6: Automation and repeatability.

(Morning: free time / Saturday market)

Afternoon (1-4pm): Introduction to automation.

Note! this will be a repeat of Friday evening! You only need to come to one.

Sunday, Day 7: Day of rest!

Monday, Day 8: Genomes, and GWAS, and k-mers.

9am lecture: Erich Schwarz, Cornell - "Assembling and biologically interpreting nematode genomes"

Morning: 10:15am-lunch, in lions & tigers & bears.

• Reference independent analyses with k-mers; sourmash. - Luiz in Lions, Phil in Tigers, and Titus in Bears.

Lunch will be local, with a food truck

Afternoon: 1pm onwards, in 1030 Valley.

• Variant calling and big genomes: GATK. (Tamer Mansour)
• Genome Wide Association Studies.
• Meta-analysis of GWAS studies (Shannon Joslin)

Evening: Ice cream and demos! 1030 Valley.

• 6:30pm onwards: ice cream!
• 7pm-9pm: demonstrations and eye candy (1030 Valley)
  • CyVerse and what an allocation request looks like.
  • Jupyter Notebook, R and Python for data science.
  • where should I put my data? One option: the Open Science Framework
  • GitHub
  • where do I find the data? NCBI, ENSEMBL, ENA; how to get FASTQ out of NCBI.
  • & other things

Tuesday, Day 9: Nanopore sequencing; and a panel discussion!

9am tutorials:

• Assessing & assembling nanopore data. (Lisa Cohen and Jon Badalamenti)
• 11am: panel discussion: The Future of Biology, Bioinformatics, and Humanity.
  • Titus' talk
  • Adrienne's talk
  • Erich's talk

4pm onwards: July 4th celebration at Community Park. We will have a sun cover and ice chests!

Wednesday, Day 10: RNAseq.

9am lecture: Megan Dennis, UC Davis - "Complex genomic variation and its role in human evolution and disease"

Morning: 10am-noon

• RMarkdown - in lions/tigers/bears rooms.

Wed 1:15-4pm: breakout sessions

• meet in 1030 Valley at 1:15pm to choose breakout sessions - see hackmd document for breakout sessions!
• move to breakout rooms on special topics.

5pm onwards: Wed market.

Thursday, Day 11: RNAseq.

9am lecture: Michael I Love, UNC Chapel Hill - "Statistics and bias correction in RNAseq differential expression analysis"

Morning (10am-noon):

• Lions: De novo RNAseq assembly - Lisa
• Tigers: DESeq2 - Mike and Rob
• Bears: ChIP-seq - Fotis and Titus

Afternoon (1:15pm-3:15pm):

• Lions: Transcriptome annotation - Camille
• Tigers: De novo RNAseq assembly - Lisa
• Bears: DESeq2 - Mike and Rob

Evening: (7pm, 1030 Valley)

• Q&A with Mike and Rob; optional.

Friday, Day 12: RNAseq.

9am lecture: Robert Patro, Stony Brook University - "Don't count on it: Pragmatic and theoretical concerns and best practices for mapping and quantifying RNA-seq data"

Morning (10am-noon):

• Lions: DESeq2 - Mike and Rob
• Tigers: ChIP-seq - Titus
• Bears: De novo RNASeq assembly - Tessa

Afternoon (1:15pm-3:15pm):

• Lions: ChIP-seq - Fotis
• Tigers: Transcriptome annotation - Camille
• Bears: Transcriptome annotation - Lisa

Saturday, last day: Summary

9am: Assessment.

9:30am lecture: C. Titus Brown, UC Davis - "Effectively infinite: next steps in Data Intensive Biology."

Further resources; continuing your learning.

Questions and answers.

Course review, input, and feedback.