The DOI matches its Crossref record; 176 of the 176 references it cites were found in a registry or an index.
From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Open accessAbstract
Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology, but a comprehensive review of the analysis tools has not been completed yet. Here, we discuss the major steps in ATAC-seq data analysis, including pre-analysis (quality check and alignment), core analysis (peak calling), and advanced analysis (peak differential analysis and annotation, motif enrichment, footprinting, and nucleosome position analysis). We also review the reconstruction of transcriptional regulatory networks with multiomics data and highlight the current challenges of each step. Finally, we describe the potential of single-cell ATAC-seq and highlight the necessity of developing ATAC-seq specific analysis tools to obtain biologically meaningful insights.
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Cites
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limma powers differential expression analyses for RNA-sequencing and microarray studies
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Cited by
Chromatin accessibility profiling by ATAC-seq
Grandi, F. C., Modi, H., Kampman, L., & Corces, M. R. (2022) · Nature Protocols · doi:10.1038/s41596-022-00692-9 · Cited by 557
“An in-depth discussion of several different applications of ATAC-seq data, and the variety of tools that are designed to accomplish them, is also reviewed by Yan et al.(103).”
MethodComprehensive analysis of single cell ATAC-seq data with SnapATAC
Fang, R., Preissl, S., Li, Y., Hou, X., Lucero, J., Wang, X., Motamedi, A., Shiau, A. K., Zhou, X., Xie, F., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21583-9 · Cited by 455
FTO mediates LINE1 m 6 A demethylation and chromatin regulation in mESCs and mouse development
Wei, J., Yu, X., Yang, L., Liu, X., Gao, B., Huang, B., Dou, X., Liu, J., Zou, Z., Cui, X.-L., et al. (2022) · Science · doi:10.1126/science.abe9582 · Cited by 294
MUON: multimodal omics analysis framework
Bredikhin, D., Kats, I., & Stegle, O. (2022) · Genome Biology · doi:10.1186/s13059-021-02577-8 · Cited by 216
Chromatin accessibility profiling methods
Minnoye, L., Marinov, G. K., Krausgruber, T., Pan, L., Marand, A. P., Secchia, S., Greenleaf, W. J., Furlong, E. E. M., Zhao, K., Schmitz, R. J., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00008-9 · Cited by 206
Metadata
- Authors
- Yan, F., Powell, D. R., Curtis, D. J., & Wong, N. C.
- Venue
- Genome Biology
- Published
- 2020-02-03
- Volume
- 21
- Issue
- 1
- Pages
- 22-22
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W3008816049
- Cited by
- 473
- References
- 176
- FWCI
- 17.98
- Type
- journal article
- Language
- en
- Open access
- gold
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