*Schedule may be subject to change closer to the course

Monday 2022-10-24

DNA methylation with Illumina 450K arrays and Bisulfite-seq

09:00 - 09:30 Welcome

09:30 - 10:15 Introduction to DNA methylation + Overview Array Exercises (slides)

10:15 - 10:30 Uppmax set-up + break

10:30 - 12:00 Exercises Array Workflow

12:00 - 13:00 lunch (offline)

13:00 - 14:00 Methylation methods & technologies (Jessica Nordlund) [slides]

14:00 - 14:15 Break

14:15 - 14:30 Methylation Exercises Overview II: Methylation Sequencing (slides)

14:30 - 16:30 Exercises Methylation Sequencing

16:30 - 17:00 Daily challenge

Tuesday 2022-10-25

ATAC-seq data processing and analysis principles

09:00 - 09:30 Recap previous day (online session)

09:30 - 10:15 Introduction to ATAC-seq data analysis (online session)

10:30 - 11.30 Exercise: Data preprocessing (online support)

11:30 - 12:00 Exercise: ATAC-seq data analysis (online support)

12:00 - 13:00 lunch (offline)

13:00 - 13.30 Motif analysis (online session)

13:30 - 15:30 Exercise: Downstream analyses (online support)

15:30 - 17:00 Exercise (offline)

16:00 - 17:00 Daily challenge

Wednesday 2022-10-26

New methods and quantitative ChIP-seq (Simon Elsässer)

09:00 - 10:00 Recap previous day (online session)

10.00 - 11.00 ChIP-seq methods (online session)

11.00 - 11.45 ChIP-seq alternatives (online session)

11.45 - 12.00 Introduction to ChIP-seq data analysis (online session)

12:00 - 13:00 lunch (offline)

13:00 - 13:30 Introduction to exercises (online session)

13:30 - 16:00 Principles of ChIP-seq and Advanced ChIP Exercises (online support)

16:00 - 17:00 Exercises (offline)

16:00 - 17:00 Daily challenge

Thursday 2022-10-27

Workflow Management Systems & inspirational talk

09:00 - 09:30 Recap previous day

09:30 - 10:00 Introduction to Workflow Management (slides)

10:00 - 10:15 break (offline)

10:15 - 10:55 nf-core exercises

11:00 - 12:00 Q & A with National Genomic Infrastructure

12:00 - 13:00 lunch (offline)

13:00 - 14:00 Determining regulatory activities of chromatin and transcription factors (Qi Dai)

14:15 - 16:00 nf-core exercises + time for earlier labs

16:00 - 17:00 Daily challenge

Friday 2022-10-28

Integrative and single cell omics

09:00 - 09:30 Recap previous day

09.30 - 10.10 Single cell methods

10.20 - 11.00 Single cell and spatially resolved epigenomics (Gonçalo Castelo-Branco)

11:15 - 12:00 Integration of genomics data

12:00 - 13:00 lunch (offline)

13.00 - 13.05 Introduction to exercises

13.05 - 15.00 Single cell and data integration exercises

15:00 - 16:00 Daily challenge

15.00 - 16.00 Course wrap-up

anytime: course feedback survey