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      Introduction to Analysis of Epigenetic Data 2020

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Introduction
Introduction to the Workshop and the Core
Schedule
What is Bioinformatics/Genomics?
Some Experimental Design?
Support
Slack
Zoom
Cheat Sheets
Software and Links
Scripts
Prerequisites
Introduction to the Command Line
Introduction to R
High Performance Computing
Data Reduction ChIPseq/ATACseq
Filetype Description
ChIP and ATAC project setup
Preprocessing Reads
Mapping Reads
Filtering Reads
Peak Call with MACS2
Data Analysis ChIPseq/ATACseq
Differential ChIPseq
Differential ATACseq
R Package Installation
Methylation
Introduction to WGBS
WGBS hands-on
ETC
Closing thoughts
Workshop Photos
Github page
Biocore website

Schedule

All posted times are Pacific time zone. At least one break will be provided each morning and afternoon.

Monday, November 30 - Prerequisite Materials

8:50 am Zoom session starts
9:00 am Welcome, format and expectations, introductions
10:00 am Recap of Introduction to Command Line
12:00 pm Lunch
1:00 pm Recap of Introduction to R
3:00 pm Using the HPC Cluster
4:00 pm Introduction to Bioinformatics
5:00 pm Zoom session ends

Tuesday, December 1 - ChIP seq and ATAC seq

8:50 am Zoom session starts
12:00 pm Lunch
5:00 pm Zoom session ends

Wednesday, December 2 - ChIP seq and ATAC seq

8:50 am Zoom session starts
12:00 pm Lunch
5:00 pm Zoom session ends

Thursday, December 3 - ChIP seq and ATAC seq, Methylation WGBS

8:50 am Zoom session starts
12:00 pm Lunch
5:00 pm Zoom session ends

Friday, December 4 - Methylation WGBS

8:50 am Zoom session starts
12:00 pm Lunch
5:00 pm Zoom session ends