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 theoretical concepts. 

TABLE OF CONTENTS

PART I - Processing raw data files

1. NCBI GEO for downloading reads, profiles and peaks

2. UCSC genome browser for visualization

PART II - Downstream analysis (genes)

3. SEQCODE for matching peaks to target genes

4. ENRICHR for gene functional analysis

PART III - Downstream analysis (peaks)

5. CHIP-ATLAS for enrichment peak analysis

6. MEME-CHIP/SEQCODE for motif analysis of peaks

PART IV - Spike-in adjustment

7. A case of study

PART I - Processing raw data files

1. NCBI GEO for downloading reads, profiles and peaks

[NCBI GEO] 

2. UCSC genome browser for visualization

[UCSC GENOME BROWSER] 

PART II - Downstream analysis (genes)

3. SEQCODE for matching peaks to target genes

[SEQCODE TOOLKIT] 

4. ENRICHR for gene functional analysis

[ENRICHR] 

PART III - Downstream analysis (peaks)

5. CHIP-ATLAS for enrichment peak analysis

[CHIP-ATLAS] 

6. MEME-CHIP/SEQCODE for motif analysis of peaks

[MEME MOTIF ANALYSIS] 

[SEQCODE TOOLKIT] 

PART IV - Spike-in adjustment

7. A case of study