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Efficient pre-processing of Single-cell ATAC-seq data

Gao, Fan and Pachter, Lior (2021) Efficient pre-processing of Single-cell ATAC-seq data. . (Unpublished)

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The primary tool currently used to pre-process 10X Chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that is 18 times faster than Cell Ranger on human samples, and that uses 33% less RAM when 8 CPU threads are used. Our tool can also calculate chromatin interaction potential matrices, and generate open chromatin signals and interaction traces for cell groups. We demonstrate the utility of scATAK in an exploration of the chromatin regulatory landscape of a healthy adult human brain and show that it can reveal cell-type-specific features. scATAK is available at

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Discussion Paper ItemscATAK Code
Gao, Fan0000-0001-6832-3402
Pachter, Lior0000-0002-9164-6231
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. We thank Xun Wang for helpful suggestions. The work was possible thanks to support by the Beckman Institute at Caltech for the Caltech Bioinformatics Resource Center. FG and LP were supported in part by NIH R01 DK126925-01. The authors have declared no competing interest.
Funding AgencyGrant Number
NIHR01 DK126925-01
Subject Keywords:single-cell, ATAC-seq, bioinformatics, open chromatin landscape, chromatin interactome
Record Number:CaltechAUTHORS:20211210-240593000
Persistent URL:
Official Citation:Efficient pre-processing of Single-cell ATAC-seq data Fan Gao, Lior Pachter bioRxiv 2021.12.08.471788; doi:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:112356
Deposited By: George Porter
Deposited On:10 Dec 2021 23:19
Last Modified:01 Feb 2022 22:54

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