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Updated: Feb 11, 2026

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A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.

Qiuchen Meng1, Xinze Wu1, Wenchang Chen1

  • 1MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China.

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|February 9, 2026
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Summary
This summary is machine-generated.

We developed consensus peaks (cPeaks), a novel chromatin accessibility reference from bulk ATAC-seq data. cPeaks improve single-cell ATAC-seq analyses, enhancing cell annotation and rare cell identification for gene regulation studies.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Single-cell ATAC-seq (scATAC-seq) advances gene regulation studies.
  • Lack of a generic ATAC-seq reference hinders single-cell analysis and cell atlas development.

Purpose of the Study:

  • To create a universal chromatin accessibility reference for scATAC-seq data.
  • To enhance cell annotation and rare cell type identification in single-cell studies.

Main Methods:

  • Aggregated 1.4 million consensus peaks (cPeaks) from 624 bulk ATAC-seq datasets.
  • Utilized a deep neural network to expand cPeaks coverage.
  • Validated cPeaks performance against existing methods in scATAC-seq analyses.

Main Results:

  • Developed cPeaks, a robust chromatin accessibility reference.
  • Demonstrated superior performance of cPeaks in scATAC-seq cell annotation and rare cell identification.
  • Showcased cPeaks' utility in studying chromatin dynamics during differentiation and tumor progression.

Conclusions:

  • cPeaks provide a consistent and comprehensive reference for chromatin accessibility.
  • This reference promotes cross-dataset consistency and accelerates biological discoveries in gene regulation.
  • cPeaks are crucial for advancing single-cell genomics and cell atlas initiatives.