index.md

SIO Nonmodel mRNASeq Workshop (2017)

These are the schedule and classroom materials for the 2017 RNAseq workshop at SIO, which will run from Oct 11-12, 2017. This will be followed by an Oct 13th lecture from instructor Lisa Komoroske as part of the Marine Biology Seminar Series.

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

If you're not comfortable working on the command line, please work through some of this command-line bootcamp before the workshop.

Schedule and Location:

All sessions are in the Eckart Sea Cave, unless otherwise noted. The workshop runs from 9am-5pm, with a 1 hour break for lunch.

Workshop materials

hackmd collaborative notes

Wednesday, Day 1: Introduction, QC, Assembly, and Quantification

• Introductions, RNA-Seq uses & pitfalls and RNAseq workflows
• Booting a cloud computer from Jetstream
• Quality trimming your reads

Lunch Break

• De novo RNAseq assembly
• Assembly evaluation
• Discussion: RNA-Seq study design

Thursday, Day 2: Differential Expression, Downstream Analyses, Alternate RNA-Seq pipelines & resources

• Quantification with Salmon
• Discussion & examples: downstream analyses

Lunch Break

• Differential Expression with DESeq2
  • Optional, on your own time: Dammit Annotation
• Discussion: Modifications & Considerations for microbial transcriptomics & metatranscriptomics
  • Clustering example
• Github + data visualization demo and git cheatsheet!
  • Optional, on your own time: Interactive github tutorial

Instructors

• Lisa Komoroske - UMass Amherst / NOAA
• Tessa Pierce - UC Davis
• Lisa Johnson - UC Davis
• John McCrow- JCVI
• Luke Thompson- NOAA

Useful Further Resources:

Note that these are taken from the 2017 ANGUS workshop and week-long DIBSI RNA-Seq workshop

Additional RNAseq:

• Lecture: Assembly evaluation
• Hands-on: Assembly evaluation
• Lecture: Annotation
• Hands-on: Transcriptome annotation
• Lecture: Quantification
• Lecture: Differential Expression

Generally useful or interesting:

• Introduction to automation

• Jupyter Notebook, R and Python for data science.

• Review and explore: Command line UNIX, and R/RStudio

• Pathway Analysis

• RMarkdown

• where do I find the data? NCBI, ENSEMBL, ENA; how to get FASTQ out of NCBI.

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

• Michael I Love, UNC Chapel Hill - "Statistics and bias correction in RNAseq differential expression analysis"

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

• C. Titus Brown, UC Davis - "Effectively infinite: next steps in Data Intensive Biology."

• Assessing & assembling nanopore data (Lisa Cohen and Jon Badalamenti)

• Using ssh to log in (instead of the web shell):

  • Log in using a password
  • OR Add ssh keys to your instance

• GitHub tutorials:

  • Lisa's tutorial
  • tutorial from ANGUS 2017

• Reference independent analyses with k-mers; sourmash.