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Higgs | Kassouf Lab Bioinformatics Documentation

This site provides resources to members of the Labaoratory of Genome Regulation Lab at the University of Oxford. These all cover foundational analysis pipelines for common genomic data types including ChIP-seq, ATAC-seq, RNA-seq and Hi-C.

There are also guides and reference links for public resources including the UCSC genome browser and GEO.

Updated: 2026-11-11T223.

Lucy Cornell and Mike Jennings.

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Chapter 1 - Using the Terminal
Learn terminal basics, the VSCode interface, and working with bed files and bedtools

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Chapter 2 - File Formats
FASTQ, SAM/BAM, IGV, GFF, and GTF file formats for genomic data

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Chapter 3 - Analysis Pipelines
Complete analysis pipelines for ATAC/ChIP-seq, RNA-seq, Capture-C, Hi-C, long-read sequencing, and genome assembly

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Chapter 4 - Using R for Genomic Data Analysis
Using R to do batch checks between samples, visualising using the plotgardener suite and performing DESeq2 analysis for differential tracks

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Chapter 5 - Making it Public
Public resources, UCSC genome browser, downloading data, and uploading to GEO

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Chapter 6 - Additional Resources
Citing bioinformatics tools, shell scripts, CGAT basics, and documentation with Quarto