ChIP-Seq-Otago-2017

ETHERPAD WITH LINKS FOR THIS WORKSHOP IS HERE:

https://beta.etherpad.org/p/H9l6EdbQfR

Analyzing ChIP-seq data - the material here is taken from https://angus.readthedocs.io/en/2017/chip-seq.html, which is based on (the material here is based on the ChIP‐seq Hands‐on Exercise, by Remco Loos and Myrto Kostadima at EMBL‐EBI, available here: https://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course/chip-seq-analysis/chip-seq-practical

The goal of the workshop is to introduce researchers to ChIP-Seq data 101 - mapping settings and calling peaks with macs2. The workshop is based on mouse data.

For this workflow, we are going to need the following tools:

1. Bowtie
2. SAMtools
3. BEDTools
4. UCSC Tools
5. MACS2
6. And for visualization, we will use ENSEMBL