Skip to content

Latest commit

 

History

History
128 lines (80 loc) · 4.13 KB

schedule-notes.md

File metadata and controls

128 lines (80 loc) · 4.13 KB
Raw

Monday

09.15 - 09.30 Introduction to the course (online session) (Olga, Agata)

09.30 - 09.45 Introduction to methylation (online session) (Vincent)

09.45 - 10.00 Break-out session (online session) (Vincent)

10.00 - 11.30 Methylation methods & technologies (online session) (Jessica Nordlund)

11.30 - 12.00 Computer exercises set-up (online support)

12.00 - 13.00 lunch (offline)

13.00 - 13.30 Methylation Exercises Overview I: Array workflow (Vincent) [internal notes: load data, QC, Normalisation, probe and region DM, GO enrichment]

13.30 - 15.30 Exercises (online support)

15.30 - 16.00 Methylation Exercises Overview II: Methylation Sequencing (Vincent)

16.00 - 17.00 Exercises (online support)

17.00 - 17.30 Test yourself (offline)

Tuesday

09.15 - 10.00 Recap of the previous day and activation exercise (online session) (Vincent)

10.00 - 11.30 Introduction to ChIP-seq & ATAC-seq (2 x 30 min, 1 break-out session) (Agata) (online session) [internal notes: intro, experimental design, data processing workflow incl. correlation, ATAC-seq]

11.30 - 13.00 lunch (offline)

13.00 - 13.30 Calling broad peaks, differential expression, motifs (online session) (Agata, Olga, Jakub)

13.30 - 15.30 Exercises (online support)

15.30 - 17.00 Exercises (offline)

17.00 - 17.30 Test yourself (offline)

Wednesday (Simon's day: needs revisit)

09.15 - 10.30 Recap of the previous day and activation exercise (group session) (online session)

10.30 - 11.30 Quantitative ChIP-seq methods (Simon)

11.30 - 13.00 lunch (offline)

13.00 - 13.30 TBD

13.00 - 15.30 Exercises (online support)

15.30 - 17.00 Exercises (offline)

17.00 - 17.30 Test yourself (offline)

Thursday

Phil / Harshil

09.15 - 10.00 Recap of the previous day (online session)

10:00 - 10:40 - Intro to Nextflow (Phil)

  • Intro to me and NGI
  • Get Nextflow, get Singularity
  • Config files
  • -resume, other core options
  • -bg to run in the background (screen, tmux)

10:40 - 11.30 - Exercises

  • Run atacseq with -profile test,uppmax
  • Rerun with -resume
  • Use nf-core launch to run

11.30 - 13.00 lunch (offline)

13:00 - 13:45 - Intro to the ChIP-seq and ATAC-seq pipelines (Harshil)

  • What they do
  • Where to find documentation
  • Run a test dataset (-profile test)
  • nf-core launch (needs testing - installed as a module?)

13.45 - 15.30 Exercises (online support)

  • Run chipseq with chr1 subset data from previous days
    • Write a sample sheet, use -r for pipeline version
  • Rerun with -resume and BroadPeaks
  • Email results with MultiQC results
  • Use nf-core launch to run with above data / sample sheet
  • Run either pipeline with nf-core AWS megatest dataset
  • Run a pipeline on their own data
  • Visual inspection of results, basic quality control and any other results based interrogation
  • Ask users to compare results to see if they are the same! Reproducible results. Woooohoooo!

TODO: Try running the subsampled test datasets from FastQ and time, using job submission with the project ID

  • Agata: Generate FastQ files from subsampled BAMs
  • Someone: Try to run exercises

TODO: Download AWS-megatest FastQ files to UPPMAX

TODO: Harshil / Phil - write up to 10 questions

  • At least one theory based
  • At least one practical (eg. listing pipelines, find latest release)

TODO: Harshil / Phil - write up the exercises in markdown on the website

15.30 - 17.00 Exercises (offline)

17.00 - 17.30 Test yourself (offline)

Friday

9.15 - 09.30 Recap of the previous day (online session)

09.30 - 10.20 scATAC-seq / scChIP-seq (Jakub) (online session, including 10 minute break)

10.20 - 10.30 Break

10.30 - 11.30 Data integration (Jakub) (online session, including 10 minute break)

11.30 - 13.00 lunch (offline)

13.00 - 13.20 Intro to exercises (online session)

13.20 - 15.00 Exercises (online support)

15.00 - 15.30 Test yourself (offline)

15.30 - 16.30 Course wrap-up (online session)