COURSES

COURSE 1. CRASH COURSE ON CHIP-SEQ BIOINFORMATIC ANALYSIS

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

[MATERIALS]

COURSE 2. High-throughput analysis of genomic data

The advent of NGS technologies has revolutionized the research in molecular biology and genetics. High-throughput analysis have emerged now as promising tools to investigate biological problems in a genome-wide context. To fully take advantage of these approaches, we introduce multiple examples of computational resources that are indispensable to gain novel knowledge from ChIP-seq and RNA-seq processing pipelines.

TABLE OF CONTENTS:

PART I - Introduction

1. The UCSC genome browser

2. The Galaxy environment

PART II - ChIPseq analysis

3. Basic pipeline (I): mapping/peak calling

4. Basic pipeline (II): genes and plots

5. Characterization of peaks

PART III - RNAseq analysis

6. Basic pipeline (I): mapping

7. Basic pipeline (II): quantification

PART IV - Past, present and future

8. Single cell RNAseq

9. Microarrays

[MATERIALS]