Analysis of ChIP-seq

(and many other DNA-seq data types)

MRC Clinical Sciences Centre

Bioinformatics Core Team

http://mrccsc.github.io/training/

What we will cover.

• Introduction to ChIP-seq.
• Analysis beginnings.
• Reads to enriched genomic regions.
• Working with signal coverage.
• Differential enrichment analysis.
• Functional analysis.
• Visualising it all.

How?

• Series of lectures.
  • Theory.
  • Practical code.
• Practical sessions.
  • On local machine
  • On AWS!

AWS?

• You should be given a URL of personal Rstudio on the cloud.
• You should have User name and password..ask if you dont.
• This is no different to standard Rstudio.
• The machine behind it is more powerful than library computers.
• This should allow us to do some real life work.

AWS - Some Rules!

• Do not start uploading data to AWS!!
  • We will have to ask you to leave the course.
• Do not use AWS for your own data analysis!!!
  • We will have to ask you to leave the course.
• Do not panic if it all goes wrong!
  • This is experimental and the course will continue locally or we will reset AWS.

AWS have given us a small grant to teach.

This allows us to do work impossible on library machines

Please dont abuse the system