ChIP-seq experiments are nowadays a solid method to build the map of binding sites of a certain antibody recognizing a transcription factor or a post-translational histone modification along the chromosomes of the genome. Here, we introduce the basic steps of the bioinformatic analysis from the FASTQ preprocessing until the downstream investigation of the resulting target genes, by embedding micro-exercises between key concepts. 

TABLE OF CONTENTS

PART I - Processing raw data files

1. NCBI GEO for downloading reads, profiles and peaks

2. GALAXY for mapping, peak calling, and exporting genome browser tracks 

3. UCSC genome browser for visualization of profiles, peaks and genes

[MATERIALS] 

PART II - Downstream analysis

4. MEME-CHIP for motif analysis of peaks

5. CHIP-ATLAS for enrichment peak analysis

6. ENRICHR for gene functional analysis

[MATERIALS] 

PART III - Spike-in adjustment

7. Spik-ChIP: a case of study

[MATERIALS]