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Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data

Genomics, Proteomics & Bioinformatics 2024年第3期22卷 11-27页

作者： Siyuan Cheng Benpeng Miao Tiandao Li Guoyan Zhao Bo Zhang Department of Developmental Biology Center of Regenerative MedicineWashington University School of MedicineSt.LouisMO 63108USA Department of Genetics Washington University School of MedicineSt.LouisMO 63108USA Department of Neurology Washington University School of MedicineSt.LouisMO 63108USA Department of Pathology and Immunology Washington University School of MedicineSt.LouisMO 63108USA

Efficient and reliable profiling methods are essential to study ***5,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 *** 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 *** methodologies can be applied to large amounts of biological samples with low-input levels,such as rare tissues,embryos,and sorted single ***,fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase ***,inappropriate data analysis can generate biased or misleading ***,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)***,we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag *** compared the sensitivity,specificity,and peak width distribution for both narrow-type and broad-type peak *** also tested the influence of the availability of control IgG input in CUT&Tag data ***,we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag *** study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies,which were implemented into Docker/Singularity images for streamlined data analysis.

关键词： tn5 transposase Epigenetic Bioinformatics ATAC-seq CUT&Tag

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