Epigenomics Analysis

Overview

Epigenomic assays show how DNA is packaged and regulated. We analyse protein binding, accessibility, nucleosome positioning and methylation across the genome.

Salient features

Peak calling, differential binding and motif analysis
Array-based and sequencing-based methylation
Integration with expression data

Analyses we offer

ChIP-seq analysis

Calls peaks, assesses quality and finds differential binding and motifs for histone marks and transcription factors.

Methods: MACS, nf-core chipseq, deepTools.

BS-seq analysis

Aligns bisulfite reads and calls methylation at single-base resolution.

Methods: Bismark, nf-core methylseq, bwa-meth.

ChIP-on-chip analysis

Analyses tiling-array ChIP data to locate protein-DNA binding regions.

Methods: Ringo, Starr.

DNA methylation array analysis

Processes Illumina methylation arrays, with normalisation, differentially methylated positions and regions.

Methods: minfi, ChAMP, sesame.

ATAC-seq analysis

Maps open chromatin and nucleosome-free regions, with footprinting and differential accessibility.

Methods: nf-core atacseq, ArchR, signac.

DNase-seq analysis

Identifies DNase hypersensitive sites and regulatory elements.

Methods: pyDNase, hotspot.

MNase-seq analysis

Maps nucleosome positions and occupancy.

Methods: nucleR, NucleoATAC.

DNA modification analysis

Detects base modifications such as 5mC directly from nanopore or PacBio signals.

Methods: modkit, nanopolish, pb-CpG-tools.

MeDIP-seq analysis

Profiles enriched methylated DNA regions from immunoprecipitation data.

Methods: MEDIPS, qsea.

MethylCap-seq analysis

Profiles methylated regions captured by methyl-binding domain proteins.