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Day 8 - Peak Calling and ChIP-Seq Analysis

Welcome to Day 8 of the Short-Read Sequencing Analysis Workshop.

 

Day 8 Videos

Video1 - Introduction to ChIP and analysis The first video will present the basic library construction steps for ChIP-Seq libraries, review the 3 types of read enrichment (point, broad, and mixed sources) and the sequencing requirements for each, and end with a brief discussion of the different goals of ChIP-Seq analysis (identify binding sites, binding motifs, target genes. function of target genes and functional domain of binding sites). Slides for Video1

Video2 - Running MACS This video will go through the analysis pipeline for calling peaks with MACS. The pipeline begins with mapping reads from fastq files (Bowtie2), converting to a sorted bam file (Samtools), and finally inputing the bam files for the ChIP sample alignment and the input control sample alignment to MACS. Slides for Video2

Video3 - Evaluating ChIP-Seq quality Slides for Video3

Video4 - Motif Analysis with MEME Slides for Video4

Day 8 Files

Day 8 In-class slides (available by start of class)

Day 8 Homework (available by start of class)

Day 8 Homework solutions (available the day after class)

Additional resources

ENCODE Guide

ENCODE ChIP-Seq Guidelines

MACS paper

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