TY - JOUR
T1 - Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data
AU - Cheng, Siyuan
AU - Miao, Benpeng
AU - Li, Tiandao
AU - Zhao, Guoyan
AU - Zhang, Bo
N1 - Publisher Copyright:
© 2024 The Author(s). Published by Oxford University Press and Science Press on behalf of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.
PY - 2024/6/1
Y1 - 2024/6/1
N2 - Efficient and reliable profiling methods are essential to study epigenetics. Tn5, one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency, is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and epigenome. Based on Tn5, the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and the Cleavage Under Targets and Tagmentation (CUT&Tag) were developed to measure chromatin accessibility and detect DNA-protein interactions. These methodologies can be applied to large amounts of biological samples with low-input levels, such as rare tissues, embryos, and sorted single cells. However, fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase quickly. Furthermore, inappropriate data analysis can generate biased or misleading conclusions. Therefore, it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&Tag data processing bioinformatics tools, many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here, we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag data. We compared the sensitivity, specificity, and peak width distribution for both narrow-type and broad-type peak calling. We also tested the influence of the availability of control IgG input in CUT&Tag data analysis. Finally, we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag data. Our study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies, which were implemented into Docker/Singularity images for streamlined data analysis.
AB - Efficient and reliable profiling methods are essential to study epigenetics. Tn5, one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency, is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and epigenome. Based on Tn5, the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and the Cleavage Under Targets and Tagmentation (CUT&Tag) were developed to measure chromatin accessibility and detect DNA-protein interactions. These methodologies can be applied to large amounts of biological samples with low-input levels, such as rare tissues, embryos, and sorted single cells. However, fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase quickly. Furthermore, inappropriate data analysis can generate biased or misleading conclusions. Therefore, it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&Tag data processing bioinformatics tools, many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here, we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag data. We compared the sensitivity, specificity, and peak width distribution for both narrow-type and broad-type peak calling. We also tested the influence of the availability of control IgG input in CUT&Tag data analysis. Finally, we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag data. Our study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies, which were implemented into Docker/Singularity images for streamlined data analysis.
KW - ATAC-seq
KW - Bioinformatics
KW - CUT&Tag
KW - Epigenetic
KW - Tn5 transposase
UR - http://www.scopus.com/inward/record.url?scp=85206018534&partnerID=8YFLogxK
U2 - 10.1093/gpbjnl/qzae054
DO - 10.1093/gpbjnl/qzae054
M3 - Article
C2 - 39255248
AN - SCOPUS:85206018534
SN - 1672-0229
VL - 22
JO - Genomics, Proteomics and Bioinformatics
JF - Genomics, Proteomics and Bioinformatics
IS - 3
M1 - qzae054
ER -