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