Analysis of Next-Generation Sequence Data

Tuesday, January 8th, 2019 – Tuesday, April 16th, 2019
Tuesdays, 12:00 PM – 3:00 PM
Location: Various, see schedule

Course Directors:

Teaching Assistants:

Project information

Project description and ideas

Class Sessions and Lecture Notes

  1. Introduction to Next Generation Sequencing | Getting to know our systems
    Tuesday, January 8th, 2019
    (class meets: BRB 204-C)

  2. Introduction to R Markdown and Unix | Homework
    Tuesday, January 15th, 2019
    (class meets: BRB 501)

  3. Sequencing technologies and library prep | Introduction to Unix continued | Introduction to project | Homework
    Boone2018 ; Thatcher2015
    Tuesday, January 22nd, 2019
    (class meets: BRB 302-D)

  4. Raw data | Data download and QC | Homework
    Zhou2014 ; Sullivan2017
    Tuesday, January 29th, 2019
    (class meets: BRB 501)

  5. Read alignment | Scripting | Homework
    STAR manual ; DelAngel2018
    Tuesday, February 5th, 2019
    (class meets: BRB 302-C)

  6. Introduction to R | Homework
    ablation.csv
    Tuesday, February 12th, 2019
    (class meets: BRB 204-C)

  7. RNA-seq data analysis | Code | Homework
    RNA-seq workshop | MultiQC report | counts file
    Tuesday, February 19th, 2019
    (class meets: BRB 302-C)

  8. RNA-seq data analysis Part II | Homework
    Code | DE code | exploratory code
    Froussios2019 ; Huang2015 ; Lin2016
    Tuesday, February 26th, 2019
    (class meets: BRB 204-C)

  9. Coding and non-coding variants
    NOTE: Monday, March 11th, 2019 (1-3pm)
    (class meets: LC 504)

  10. Single cell RNA-seq | Homework
    WT-1.dge.txt.gz
    Andrews2018 ; Crow2018 ; Lafzi2018 ; CellType2017 ; Ziegenhain2017
    Tuesday, March 19th, 2019
    (class meets: BRB 204-A)

  11. Other NGS technologies | Homework
    Nanopore Sequencing Recap | minION QC | NanoPlot Report
    Jain2014 ; Wick2019
    Tuesday, March 26th, 2019
    (class meets: BRB 204-C)

  12. Sequencing core facility
    Tuesday, April 2nd, 2019
    (class meets: TBA)

  13. ChIP-seq/ATAC-seq
    Tuesday, April 9th, 2019
    (class meets: WGC-C)
    Klemm2019 ; Meyer2014 ; Winter2015

  14. Student presentations
    Tuesday, April 16th, 2019
    (class meets: BRB 302-C)