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ScATAC-seq Analysis

ScATAC-seq Analysis

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As one of the providers of scATAC-seq analysis, CD Genomics uses bioinformatics to help you carefully select algorithmic approaches and parameters for each step of your data analysis pipeline in order to reliably translate chromatin accessibility information into new biological hypotheses. Our high-quality data analysis platform will be used to generate high-quality analysis results in a fast analysis cycle.

Research Advances in ScATAC-seq Analysis

The majority of genetic variation associated with complex human traits is located in non-coding genomic regions. Thus, understanding the genotype-to-phenotype axis requires a comprehensive catalog of functional non-coding genomic components, most of which are involved in epigenetic regulation of gene expression. With the advent of single-cell biology and the application of various sequencing-based histological techniques, it has become possible to study chromatin accessibility at single-cell resolution due to the development of single-cell ATAC sequencing (scATAC-seq). However, computational analysis of scATAC-seq data remains challenging. In addition, various potential functional elements within accessible genomic regions can increase the complexity of interpreting scATAC-seq data if the scATAC-seq data is not well understood. Recently, computational algorithms and software tools have been developed for scATAC-seq data analysis, such as SnapATAC.

Fig. 1. Schematic overview of a typical single-cell ATAC sequencing analysis workflow.Fig. 1. Schematic overview of a typical single-cell ATAC sequencing analysis workflow. (Baek S, et al, 2020)

Application Field

Our scATAC-seq analysis can be used for but not limited to the following research:

Developmental biology: our scATAC-seq analysis can reveal dynamic changes in chromatin accessibility during embryogenesis, greatly contributing to our understanding of developmental processes. It is able to identify cis-regulatory elements that coordinate spectral specification and tissue-specific gene expression patterns. By studying the chromatin accessibility landscape at different developmental stages, we help you gain insight into the molecular mechanisms of tissue morphogenesis and cell differentiation.

Disease studies:by comparing chromatin accessibility profiles between healthy and diseased cells, we can help you identify disease-specific regulatory elements and gain insight into dysregulation of gene expression programs. This information may lead to the discovery of new therapeutic targets and the development of precision medicine approaches, including cancer, neurological disorders and immune-related diseases

Cell type classification and genealogy tracking:our scATAC-seq analysis enables the classification and identification of different cell populations based on chromatin accessibility profiles. This information facilitates cell type characterization, lineage tracing, and discovery of cell-specific regulatory elements.

Immune system analysis:our scATAC-seq analysis provides a powerful tool to analyze the epigenetic landscape of immune cells, enabling the characterization of cell types, identification of regulatory elements involved in the immune response, and exploration of immune cell differentiation trajectories.

CD Genomics Data Analysis Pipeline:

CD Genomics is at the forefront of scATAC-seq analysis, providing a comprehensive service to researchers worldwide. Our team of experienced scientists and bioinformaticians are well versed in the intricacies of scATAC-seq data and offer tailored solutions for a wide range of research objectives. Our services cover the entire workflow of scATAC-seq analysis from pre-processing to data analysis.

(1) Data pre-processing and quality control

CD Genomics uses state-of-the-art tools and algorithms to pre-process scATAC-seq data, including read alignment, duplicate removal, and quality control. By ensuring high quality data, we lay a solid foundation for downstream analysis.

(2) Peak calling and annotation

CD Genomics utilizes advanced peak calling algorithms to accurately detect chromatin accessibility peaks in individual cells. In addition, we employ a comprehensive annotation pipeline to correlate these peaks with known regulatory elements and genomic features.

(3) Cell clustering and cell type identification

CD Genomics uses powerful clustering algorithms to identify distinct cell populations based on chromatin accessibility profiles. Through integrated analysis with other histological data (e.g. scRNA-seq), we can assign cell types and further dissect the regulatory landscape within specific cell populations.

(4) Differential accessibility analysis

To elucidate the regulatory dynamics between different cell types or conditions, CD Genomics provides differential accessibility analysis. By comparing chromatin accessibility profiles between cell groups, we can identify differentially accessible regions associated with specific biological processes or disease states. This information provides valuable insights into the functional implications of epigenetic changes.

(5) Trajectory analysis

CD Genomics uses sophisticated trajectory analysis algorithms to reconstruct cellular trajectories based on chromatin accessibility data. By inferring the developmental pathways of cells, we can gain insight into the regulatory events that drive cell fate decisions.

ScATAC-seq Analysis Content:

Data Pre-Processing Preprocessing of sequencing reads
Quality control
Formation of feature-by-feature matrix
Batch calibration and data integration
Batch calibration and data integration
Dimensionality reduction, visualization and clustering
Hypothesis Generation for Downstream Analysis Cell identity annotation
Chromatin accessibility kinetics study
Hypothesis generation based on TF motif
Gene based hypothesis generation
Hypothesis generation based on enhancer
Hypothesis generation for disease-associated genetic variants
Integrated Analysis with Single Cell Transcriptome Data Combined analysis of multi-modal data will help to detect correlations between trans and cis regulatory elements in the cellular state of interest

How It Works

CD Genomics is a high-tech company specializing in multiomic data analysis. We provide services such as project design, data analysis, and database construction. With a focus on developing breakthrough products and services, we are a pioneer in the biotechnology industry, serving researchers and partners worldwide.

How It Works

CD Genomics provides scATAC-seq data analysis to explore individual cellular regulatory patterns and more. With our expertise, advanced technology, and commitment to quality, we enable researchers to gain valuable insights into cellular heterogeneity, regulatory mechanisms, and disease processes. Collaborate with CD Genomics for accurate and comprehensive scATAC-seq analysis to move your research forward. If you are interested in our services, please contact us for more detailed information.


  1. Baek S, Lee I. Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation[J]. Computational and structural biotechnology journal, 2020, 18: 1429-1439.
* For Research Use Only. Not for use in diagnostic procedures.
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