CUT&RUN / CUT&Tag
Quantitative profiling of protein–DNA interactions
CUT&RUN and CUT&Tag enable high-resolution profiling of protein–DNA interactions using targeted nuclease cleavage, producing low-background datasets from minimal input material. Standard workflows incorporate E. coli carry-over or spike-in DNA as an internal reference, allowing normalisation across samples and improving quantitative comparability between conditions.
Careful analysis of CUT&RUN or CUT&Tag data can reveal biologically meaningful binding patterns, chromatin states, and regulatory elements while accounting for technical variation introduced during library preparation and sequencing. Incorporating appropriate normalisation and QC increases confidence in peak detection and downstream interpretation, supporting robust and reproducible epigenomic conclusions without additional experimental work.
€ Priced based on project discussion(s). Get in touch:
Details
This service is for the FASTQ data processing, QC reports, and minimal biological or statistical interpretation.
Optional add-ons such as figure preparation, or data upload to public repositories, are available on request.
Project Setup
• Includes project discussions and data transfers
Analysis per Sample
• Suitable for 1 to >100 samples
NCBI Submission
• FASTQ FTP upload to generate BioProject and Accession IDs
Video Discussions – n=3
• Kick-off, update, and wrap-up calls
Turnaround Time – 2–3 weeks
• Queue and project size dependent
Delivery – Dropbox / FileZilla
• Data retained for 30 days
Deliverables
All files are shared via secure, GDPR-compliant data transfers.
Data upload and release will be organised via Dropbox or Filezilla.
Compute resources are provided by an Irish-based cloud computing provider, CloudCIX.
multiqc_report.html
• Aggregated quality control summary of raw and processed sequencing data
aligned_reads
• Genome-aligned and filtered sequencing reads for each sample
signal_tracks
• Normalised genome-wide signal tracks suitable for visualisation
enrichment_regions
• Genomic regions showing enriched signal relative to background
quantitative_matrix.csv
• Quantitative signal per genomic region (rows) per sample (columns)
Requirements
Pipelines can be run on (i) newly generated datasets, (ii) publicly available metagenomes, or (iii) a combination of both, enabling comparative analyses across studies and environments.
This flexibility allows integration of novel samples with existing resources for broader context and reproducibility.
Input Format
• Paired- or single-end FASTQ (gzipped)
Read Length
• 50–150 bp
Depth
• ≥ 3 Mn reads
Optional Preprocessing
• Read repair – BBTools
Accepted Platforms
• Illumina, MGI, Element Biosciences, Ultima Genomics
Technical
All analyses are executed within isolated Conda environments, ensuring full reproducibility and dependency control across runs.
Each tool and database version is tracked, guaranteeing consistent results between projects and over time.
QC
• Tool(s): FastQC v0.12
• Purpose: Per-sample read quality analysis
Reporting
• Tool(s): MultiQC v1.31
• Purpose: Combined QC report
Trimming
• Tool(s): fastp v0.23
• Purpose: Adapter and low-quality trimming
Host Removal
• Tool(s): Kraken2 v2.0.8
• Purpose: Optional; host genome or taxonomy database required
Deduplication
• Tool(s): Clumpify v39.33
• Purpose: Duplicate read removal
Read Mapping
• Tool(s): Bowtie2
• Purpose: Short-read mapping to known databases
Workflow
Client data are transferred securely to BioFigR via Dropbox/Filezilla and processed on CloudCIX infrastructure using rsync. All transfers occur within GDPR-compliant environments, with optional deposition to NCBI via FTP only upon client approval. No data are shared or stored beyond the agreed workflow stages.
Contact BioFigR
This streamlined, reproducible nf-core/cutandrun pipeline ensures data integrity from upload to analysis. BioFigR provides transparent, compliant handling at every stage—so clients can focus on results, not logistics.
Contact BioFigR with the number of samples and reads per sample to receive a quotation, or to discuss project requirements.