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Using MACS to Identify Peaks from ChIP‐Seq Data
Open accessAbstract
Model‐based Analysis of ChIP‐Seq (MACS) is a command‐line tool designed by X. Shirley Liu and colleagues to analyze data generated by ChIP‐Seq experiments in eukaryotes, especially mammals. MACS can be used to identify transcription factor binding sites and histone modification–enriched regions if the ChIP‐Seq data, with or without control samples, are given. This unit describes two basic protocols that provide detailed information on how to use MACS to identify either the binding sites of a transcription factor or the enriched regions of a histone modification with broad peaks. Furthermore, the basic ideas for the MACS algorithm and its appropriate usage are discussed. Curr. Protoc. Bioinform. 34:2.14.1‐2.14.14. © 2011 by John Wiley & Sons, Inc.
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High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
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Dominissini, D., Moshitch-Moshkovitz, S., Salmon-Divon, M., Amariglio, N., & Rechavi, G. (2013) · Nature Protocols · doi:10.1038/nprot.2012.148 · Cited by 710
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Disruption of DNA-methylation-dependent long gene repression in Rett syndrome
Gabel, H. W., Kinde, B., Stroud, H., Gilbert, C. S., Harmin, D. A., Kastan, N. R., Hemberg, M., Ebert, D. H., & Greenberg, M. E. (2015) · Nature · doi:10.1038/nature14319 · Cited by 569
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Nord, A. S., Blow, M. J., Attanasio, C., Akiyama, J. A., Holt, A., Hosseini, R., Phouanenavong, S., Plajzer-Frick, I., Shoukry, M., Afzal, V., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.033 · Cited by 375
Metadata
- Authors
- Feng, J., Liu, T., & Zhang, Y.
- Venue
- Current Protocols in Bioinformatics
- Publisher
- Wiley
- Published
- 2011-06
- Volume
- 34
- Issue
- 1
- Pages
- 2.14.1-2.14.14
- ISSN
- 1934-3396 (ISSN-L)
- 1934-340X
- OpenAlex
- W1585888846
- Cited by
- 252
- References
- 3
- FWCI
- 5.76
- Type
- journal article
- Language
- en
- Open access
- green
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