CUT&RUN and CUT&TAG Analysis

What is ATAC sequencing?

Basepair provides a point & click graphical user interface to the industry standard tools needed to analyze this type of data (such as Bowtie2, SEACR, Homer and MACS2) so you don’t have to spend time figuring out how to run them yourself.

• 1. Easy as 1, 2, 3: Upload, analyze, visualize.

Basepair wanted to make CUT&RUN and CUT&TAG data analysis so simple that users with no programming experience, or the time to wait for days for results, could run our automated pipelines. Data upload is easy. Just drag and drop files, connect directly to Basespace or use your own cloud storage bucket.

If an interesting relationship or trend in the data is observed in one of the visualizations in our interactive reports, then maybe that’s the time to collaborate with a bioinformatician on an informed question.

• 2. Transparency & Reproducibility with Industry Standard Tools

Basepair platform was designed for reproducibility and transparency — from QC and read charts, to interactive plots ready for publication. All CUT&RUN and CUT&TAG tools available in their platform are industry standard algorithms that have been highly cited and peer-reviewed. They include:

• Bowtie2 is a fast and accurate alignment tool that aligns the high-quality reads to a reference genome or assembly with high sensitivity and specificity. It is designed to handle a wide range of read lengths and is suitable for analyzing CUT&RUN and CUT&TAG NGS data from various organisms and experimental conditions.
• SEACR (Signal Extraction for Autocorrelated Regions) is a tool specifically designed for CUT&RUN and CUT&TAG NGS data analysis. It extracts the signal from the data and identifies enriched regions with high sensitivity and specificity. SEACR also corrects for the autocorrelation inherent in such data, resulting in more accurate peak calling and improved downstream analysis.
• Homer is a suite of tools for analyzing ChIP-seq as well as CUT&RUN and CUT&TAG NGS data. It includes tools for motif discovery, peak calling, and differential analysis. Homer’s peak calling algorithm uses a dynamic background model to accurately identify peaks, even in noisy data. It also includes tools for functional annotation, including gene ontology and pathway analysis.
• MACS2 (Model-based Analysis of ChIP-Seq 2) is another popular tool for peak calling in both ChIP-seq as well as CUT&RUN and CUT&TAG NGS data. It uses a probabilistic model to identify peaks and includes a number of options for peak calling and peak filtering. MACS2 also includes tools for visualization, annotation, and differential analysis.

• 3. Commercial Grade Software at an Affordable Price

Let’s face it, no one likes annual software licenses unless you need to process large
sample volumes. Contact any of our Sales Representatives

• 4. More Than Just Flat File Outputs

All of the intermediary files are made available for download. All graphs and figures can also be downloaded as high quality, ready-for-publication images to make writing that paper or creating that powerpoint just a little bit easier. Otherwise, all of the interactive visualizations update dynamically as you change the parameters & thresholds, allowing you to explore your data at length to facilitate that next scientific insight.