Principles of ChIP-seq Data Analysis Illustrated with Examples

2015 ◽  
Vol 1 (1) ◽  
pp. 22 ◽  
Author(s):  
Giovanna Ambrosini ◽  
René Dreos ◽  
Philipp Bucher
Keyword(s):  
Data Analysis ◽  
Next Generation Sequencing ◽  
Chromatin Immunoprecipitation ◽  
Powerful Method ◽  
Associated Proteins ◽  
On Chip ◽  
Chromatin Profiling ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Regulate Gene

Chromatin immunoprecipitation (ChIP) followed by highthroughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single ChIPseq experiment produces large amounts of highly reproducible data. The challenge is to extract knowledge from the data by thoughtful application of appropriate bioinformatics tools. Here we present a concise introduction into ChIP-seq data analysis in the form of a tutorial based on tools developed by our group. We expose biological questions, explain methods and provide guidelines for the interpretation of the results. While this article focuses on ChIP-seq, most of the algorithms and tools we present are applicable to other chromatin profiling assays based on next generation sequencing (NGS) technology as well.

scholarly journals Applications and data analysis of next-generation sequencing

2013 ◽  
Vol 37 (6) ◽  
Author(s):  
Ina Vogl ◽  
Anna Benet-Pagès ◽  
Sebastian H. Eck ◽  
Marius Kuhn ◽  
Sebastian Vosberg ◽  
...  
Keyword(s):  
Data Analysis ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
High Expectations ◽  
Sequencing Platform ◽  
Software Products ◽  
High Throughput Method ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Enrichment Methods

Abstract:Over the past 6 years, next-generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. Although the high expectations regarding the discovery of new diagnostic targets and an overall reduction of cost have been achieved, technological challenges in instrument handling, robustness of the chemistry, and data analysis need to be overcome. Each workflow and sequencing platform have their particular problems and caveats, which need to be addressed. Regarding NGS, there is a variety of different enrichment methods, sequencing devices, or technologies as well as a multitude of analyzing software products available. In this manuscript, the authors focus on challenges in data analysis when employing different target enrichment methods and the best applications for each of them.

scholarly journals An Overview of RNA-seq Data Analysis

2017 ◽  
Vol 8 (2) ◽  
pp. 57
Author(s):  
Tahsin Ferdous ◽  
Mohammad Ohid Ullah
Keyword(s):  
Data Analysis ◽  
Next Generation Sequencing ◽  
High Throughput ◽  
Microarray Data ◽  
Positive Outcomes ◽  
Rna Seq ◽  
Specific Time ◽  
High Throughput Dna Sequencing ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Latest breakthrough in high-throughput DNA sequencing have been launched different arenas for transcriptome analyses, jointly named RNA-seq (RNA-sequencing). It exposes the existence and amount of RNA in a biotic sample at a specific time by utilizing next generation sequencing (NGS). In this review, we aimed to explore the several methods which are applied in analyzing RNA-seq data. We also discussed its importance over microarray data. As establishment of several methods have already taken place to analyze RNA-seq data, therefore, further analysis is very essential to select the best one to avoid false positive outcomes.

Characterization of sequence-specific errors in various next-generation sequencing systems

2016 ◽  
Vol 12 (3) ◽  
pp. 914-922 ◽  
Author(s):  
Sunguk Shin ◽  
Joonhong Park
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Ecology ◽  
Scientific Basis ◽  
Poor Quality ◽  
Powerful Method ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS) is a powerful method for functional microbial ecology in a variety of environments including human's body. In this work, novel sequence-specific errors (SSEs) from the currently popular NGS systems and their hotspots were discovered, providing a scientific basis for filtering poor-quality sequence reads from the different NGS systems.

scholarly journals De Novo Assembly-Based Analysis of RPGR Exon ORF15 in an Indigenous African Cohort Overcomes Limitations of a Standard Next-Generation Sequencing (NGS) Data Analysis Pipeline

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 800
Author(s):  
Jordi Maggi ◽  
Lisa Roberts ◽  
Samuel Koller ◽  
George Rebello ◽  
Wolfgang Berger ◽  
...  
Keyword(s):  
Data Analysis ◽  
Next Generation Sequencing ◽  
De Novo Assembly ◽  
De Novo ◽  
African Ancestry ◽  
Secondary Analysis ◽  
Next Generation ◽  
Analysis Pipeline ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

RPGR exon ORF15 variants are one of the most frequent causes for inherited retinal disorders (IRDs), in particular retinitis pigmentosa. The low sequence complexity of this mutation hotspot makes it prone to indels and challenging for sequence data analysis. Whole-exome sequencing generally fails to provide adequate coverage in this region. Therefore, complementary methods are needed to avoid false positives as well as negative results. In this study, next-generation sequencing (NGS) was used to sequence long-range PCR amplicons for an IRD cohort of African ancestry. By developing a novel secondary analysis pipeline based on de novo assembly, we were able to avoid the miscalling of variants generated by standard NGS analysis tools. We identified pathogenic variants in 11 patients (13% of the cohort), two of which have not been reported previously. We provide a novel and alternative end-to-end secondary analysis pipeline for targeted NGS of ORF15 that is less prone to false positive and negative variant calls.

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