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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

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

Min Li¹, Li Tang², Fang-Xiang Wu³

¹School of Computer Science and Engineering, Central South University, Changsha, China. limin@mail.csu.edu.cn.

BMC Bioinformatics

|December 26, 2019

Summary

ChIP-Seq Analysis (CSA) is a new web service offering comprehensive, user-friendly analysis of ChIP-seq data from raw processing to downstream applications. CSA visualizes results and identifies binding sites, simplifying complex genomic analyses.

Keywords:

ChIP-seq Downstream analysis Peak calling Quality control Visualization

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Last Updated: Jan 1, 2026

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

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Published on: April 11, 2016

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Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells

Published on: December 10, 2014

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Chromatin immunoprecipitation sequencing (ChIP-seq) is crucial for analyzing DNA-protein interactions.
Current ChIP-seq analysis tools often lack user-friendly interfaces and comprehensive workflows.
Existing web services do not offer end-to-end analysis from raw data to downstream applications.

Purpose of the Study:

To develop a comprehensive, user-friendly web service for the entire ChIP-seq analysis pipeline.
To provide visualization tools for various analysis steps, including mapping, peak calling, and motif finding.
To enable detection of differential ChIP signals for identifying absolute DNA-protein binding sites.

Main Methods:

Development of a web service named ChIP-Seq Analysis (CSA).
Integration of modules for data mapping, quality control, peak calling, and downstream analysis.
Implementation of customization options for user-defined workflows and visualization of results.

Main Results:

CSA provides a complete workflow for ChIP-seq data analysis through a web interface.
The service includes visualization for mapping, peak calling, motif finding, and pathway analysis.
CSA effectively identifies absolute binding sites by comparing ChIP samples with controls.

Conclusions:

CSA offers an effective, end-to-end solution for ChIP-seq analysis via a web interface.
The platform visualizes each analysis step, enhancing user understanding and usability.
Case studies confirm CSA's effectiveness in completing the entire ChIP-seq analysis procedure.