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Bioinformatics core workflow for ChIP-seq data analysis.
In: Chromatin Immunoprecipitation. Berlin [u.a.]: Springer, 2024. 47-62 (Methods Mol. Biol. ; 2846)
Chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (-seq) has been the most common genomics method for studying DNA-protein interactions in the last decade. ChIP-seq technology became standard both experimentally and computationally. This chapter presents a core workflow that covers data processing and initial analytical steps of ChIP-seq data. We provide a step-by-step protocol of the commands as well as a fully assembled Snakemake workflow. Along the protocol, we discuss key tool parameters, quality control, output reports, and preliminary results.
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Publication type
Article: Edited volume or book chapter
Keywords
Automated Workflow ; Chip-seq ; Chromatin Biology ; Quality Control ; Reproducibility ; Step-by-step Protocol
Language
english
Publication Year
2024
HGF-reported in Year
2024
ISSN (print) / ISBN
1064-3745
e-ISSN
1940-6029
Book Volume Title
Chromatin Immunoprecipitation
Journal
Methods in Molecular Biology
Quellenangaben
Volume: 2846,
Pages: 47-62
Publisher
Springer
Publishing Place
Berlin [u.a.]
Reviewing status
Peer reviewed
Institute(s)
Institute of Epigenetics and Stem Cells (IES)
POF-Topic(s)
30204 - Cell Programming and Repair
Research field(s)
Stem Cell and Neuroscience
PSP Element(s)
G-506200-001
PubMed ID
39141229
Erfassungsdatum
2024-10-01