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ChIP-Sequencing / CUT&RUN / CUT&TAG

How Projects Run

All ChIP-seq, CUT&RUN, and CUT&TAG projects are scoped individually to ensure the analysis strategy is appropriate for the assay, target, and biological question.

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  • Initial project planning meeting

An online discussion to review experimental design, controls, spike-ins (if applicable), sequencing depth, and downstream goals before analysis begins.

  • Transparent, reproducible analysis

Analyses are performed using fully documented, reproducible pipelines, with clear communication around key decisions such as filtering thresholds, peak calling strategy, and normalisation.

  • Results review and next steps

A final meeting to walk through results, visualisations, and biological interpretation, with guidance on validation, comparative analyses, or publication preparation.

Raw Data Processing

Starting from £40 per sample

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  • Processing of single-end or paired-end ChIP-seq, CUT&RUN, or CUT&TAG data using reproducible workflows built with Conda, Python, and Snakemake

  • Alignment to the appropriate reference genome, with optional spike-in alignment and normalisation

  • Comprehensive quality control including FASTQC, alignment statistics, cross-correlation, fragment size distribution, and enrichment metrics

  • Filtering for properly paired reads, removal of duplicates, and blacklist region filtering

  • Generation of normalised BigWig files for interactive genome browser visualisation

  • Peak calling using MACS2 at both relaxed and stringent thresholds

  • IDR analysis to identify reproducible peaks across biological replicates

  • Fixed software versions and documented parameters to ensure full reproducibility

  • Standard pipelines that can be customised to assay type, target class, or experimental design

ChIP-seq snakemake workflow showing sequencing QC, alignment, normalization, peak calling, and MultiQC reporting steps.

Basic Peak & Enrichment Analysis

Processing + basic analysis from £70 per sample

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Includes everything in Raw data processing, plus:

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  • Annotation of peaks to genomic features (promoters, enhancers, intronic/intergenic regions)

  • Signal heatmaps and average profiles around transcription start sites, peak centres, or user-defined regions

  • Genome browser snapshots for representative loci

  • Comparative peak overlap analyses between conditions

  • Clear, annotated results tables summarising peak statistics

  • Results meeting to discuss interpretation and biological relevance

Advanced Analysis

Processing + basic + advanced analysis from £110 per sample

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Includes everything in Basic peak and enrichment analysis, plus:

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  • Differential binding or occupancy analysis between conditions

  • Motif discovery and enrichment analysis using HOMER and/or MEME-suite

  • Integration with RNA-seq or other omics data (where available)

  • Chromatin state or regulatory element-focused analyses

  • Pathway or gene-set enrichment based on peak-associated genes

  • Iterative development of publication-ready figures and supplementary materials

  • Support with biological interpretation and results framing

Packages are available for complete project support, from raw data processing through to publication-ready results.

All prices are indicative and may vary depending on experimental design, dataset size, species, and analytical scope. Academic and multi-sample project discounts are available.

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