Schedule 2020

Analysis of Next-Generation Sequence Data

Tuesday, January 7th, 2020 – Tuesday, April 14th, 2020
Tuesdays, 12:00 PM – 3:00 PM
Location: Various, see schedule

Course Directors:

• Friederike Dündar (frd2007@med.cornell.edu)
• Luce Skrabanek (las2017@med.cornell.edu)

Teaching Assistants:

• Mervin Fansler (mef3005@med.cornell.edu)
  Office hours: Thursdays 3:00 PM - 4:00 PM; Archbold Commons (2nd Floor of 1300 York Ave).

Project information

Project description and ideas

Class Sessions and Lecture Notes

1. Introduction to Unix | Getting to know our systems
   Tuesday, January 7th, 2020
   (class meets: BRB 302-C)

2. Introduction to Next Generation Sequencing | Introduction to R Markdown and git | Homework
   Tuesday, January 14th, 2020
   (class meets: BRB 302-B)

3. Sequencing technologies and library prep | Introduction to Unix continued | Introduction to project | Homework
   Boone2018 ; Thatcher2015
   Tuesday, January 21st, 2020
   (class meets: BRB 302-B)

4. Raw data | Data download and QC | Homework
   Zhou2014 ; Sullivan2017
   Tuesday, January 28th, 2020
   (class meets: BRB 302-A)

5. Introduction to R | Homework
   Code quality | R styles | ablation.csv
   Tuesday, February 4th, 2020
   (class meets: BRB 302-B)

6. Read alignment | Running STAR and BWA | Homework
   STAR manual ; DelAngel2018 ; Ballouz2019
   Tuesday, February 11th, 2020
   (class meets: WGC-C)

7. RNA-seq data analysis | Homework
   RNA-seq workshop | MultiQC report | counts file
   Stark2019
   Tuesday, February 18th, 2020
   (class meets: BRB 302-B)

8. RNA-seq data analysis Part II | Homework
   DGE_background | DGE_code_01 | DGE_code_02 | DGE_code_03
   Additional DGE-related scripts
   RNA-seq Gierlinski RData | Lecture Part B
   Froussios2019 ; Huang2015 ; Lin2016
   Tuesday, February 25th, 2020
   (class meets: WGC-B)

9. Spring break; no class

10. Coding and non-coding variants
    Homework
    NOTE: Monday, March 9th, 2020 (1-3pm)
    (class meets: LC 504)

11. Single cell RNA-seq | Homework | Data set
    Andrews2018 ; Crow2018 ; Lafzi2018 ; CellType2017 ; Ziegenhain2017
    Tuesday, March 17th, 2020

12. Sequencing core facility | Homework
    Tuesday, March 24th, 2020

13. ChIP-seq/ATAC-seq | Homework
    Klemm2019 ; Meyer2014 ; Winter2015 ; Yan2020
    Tuesday, March 31st, 2020

14. Other NGS technologies
    Tuesday, April 7th, 2020

15. Student presentations
    Tuesday, April 14th, 2020
    (class meets: BRB 302-C)