CSA：一个用于 ChIP-Seq 分析完整流程的网络服务。

CSA: a web service for the complete process of ChIP-Seq analysis.

机构信息

School of Computer Science and Engineering, Central South University, Changsha, China.

Division of Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan, SKS7N5A9, Saskatoon, Canada.

出版信息

BMC Bioinformatics. 2019 Dec 24;20(Suppl 15):515. doi: 10.1186/s12859-019-3090-0.

DOI:10.1186/s12859-019-3090-0

PMID:31874601

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6929326/

Abstract

BACKGROUND

Chromatin immunoprecipitation sequencing (ChIP-seq) is a technology that combines chromatin immunoprecipitation (ChIP) with next generation of sequencing technology (NGS) to analyze protein interactions with DNA. At present, most ChIP-seq analysis tools adopt the command line, which lacks user-friendly interfaces. Although some web services with graphical interfaces have been developed for ChIP-seq analysis, these sites cannot provide a comprehensive analysis of ChIP-seq from raw data to downstream analysis.

RESULTS

In this study, we develop a web service for the whole process of ChIP-Seq Analysis (CSA), which covers mapping, quality control, peak calling, and downstream analysis. In addition, CSA provides a customization function for users to define their own workflows. And the visualization of mapping, peak calling, motif finding, and pathway analysis results are also provided in CSA. For the different types of ChIP-seq datasets, CSA can provide the corresponding tool to perform the analysis. Moreover, CSA can detect differences in ChIP signals between ChIP samples and controls to identify absolute binding sites.

CONCLUSIONS

The two case studies demonstrate the effectiveness of CSA, which can complete the whole procedure of ChIP-seq analysis. CSA provides a web interface for users, and implements the visualization of every analysis step. The website of CSA is available at http://CompuBio.csu.edu.cn.

摘要

背景

染色质免疫沉淀测序（ChIP-seq）是一种将染色质免疫沉淀（ChIP）与下一代测序技术（NGS）相结合的技术，用于分析蛋白质与 DNA 的相互作用。目前，大多数 ChIP-seq 分析工具采用命令行，缺乏用户友好的界面。尽管已经开发了一些具有图形界面的用于 ChIP-seq 分析的网络服务，但这些站点无法从原始数据到下游分析提供对 ChIP-seq 的全面分析。

结果

在本研究中，我们开发了一个用于 ChIP-Seq 分析（CSA）全过程的网络服务，涵盖了映射、质量控制、峰调用和下游分析。此外，CSA 为用户提供了自定义功能，以定义自己的工作流程。CSA 还提供了映射、峰调用、基序发现和途径分析结果的可视化。对于不同类型的 ChIP-seq 数据集，CSA 可以提供相应的工具来执行分析。此外，CSA 可以检测 ChIP 样本和对照样本之间 ChIP 信号的差异，以识别绝对结合位点。