Methods for ChIP-seq analysis: A practical workflow and …
2021年3月1日 · We focus on practical, rather than theoretical, approaches for biological studies. Next, we outline various advanced ChIP-seq applications and introduce several state-of-the-art methods, including prediction of gene expression level and chromatin loops from epigenome data and data imputation.
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data …
2013年11月14日 · We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis.
A step-by-step guide to ChIP-seq data analysis. December 03, 2014. Xi Chen, Ph.D. EMBL-European Bioinformatics Institute Wellcome Trust Sanger Institute. Wet-lab biologists with no experience of programming and Unix/Linux environment. ChIP-seq beginners. Raw sequencing reads (fastq files)
Basics of ChIP-seq data analysis - Bioconductor
This vignette describes steps of a basic analysis of ChIP-seq data. To exemplify this tutorial, we use ChIP-seq data for the lysine 27 acetylation of the histone H3 (i.e H3K27ac).
A complete workflow for the analysis of full-size ChIP-seq
2012年7月26日 · The workflow combines four word-based pattern-discovery algorithms that rely on two complementary criteria (overrepresentation and positional bias) to detect exceptional words (oligonucleotides ...
Best practices for ChIP-seq and its data analysis - ScienceDirect
2024年1月1日 · This chapter describes how best to design a ChIP-seq experiment based on your cell or tissue type of choice, your protein target of choice, and how much material you are starting with, and follows with the best practices in downstream data analysis after sequencing.
The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq ...
2016年11月18日 · Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware.
Bioinformatics Core Workflow for ChIP-Seq Data Analysis
2024年8月15日 · 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.
A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages
2017年3月29日 · Now, the standard ChIP-Seq data analysis process consists of a quality check (QC), mapping, peak calling, statistical analysis, annotation, and visualization.
In this brief tutorial we will learn how to use the excellent tool Galaxy (http://galaxyproject.org/) to analyse data from a chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiment. It is part of a series of introductory tutorials that can be found at http://sschmeier.github.io/bioinf-workshop/.