Deep Sequencing Data Analysis

ISBN-13: 9781627035132 / Angielski / Twarda / 2013 / 234 str.

Noam Shomron

Opis

The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. Effectively, when carefully planned, any experimental question which can be translated into reading nucleic acids can be applied.In Deep Sequencing Data Analysis, expert researchers in the field detail methods which are now commonly used to study the multi-facet deep sequencing data field. These included techniques for compressing of data generated, Chromatin Immunoprecipitation (ChIP-seq), and various approaches for the identification of sequence variants. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data analysis procedures for deep sequencing data interpretation.

Spis treści

1. An Introduction to High-throughput Sequencing Experiments: Design and Bioinformatics Analysis

Rachelly Normand and Itai Yanai

 2. Compressing Resequencing Data with GReEn ∗

Armando J. Pinho Diogo Pratas Sara P. Garcia

 3. On the Accuracy of Short Read Mapping

Peter Menzel , Jes Frellsen , Mireya Plass, Simon H. Rasmussen, and  Anders Krogh

 4. Statistical Modeling of Coverage in High-Throughput Data

David Golan and Saharon Rosset

 5. Assembly Algorithms for Deep Sequencing Data: Basics and Pitfalls

Nitzan Kol and Noam Shomron

6. Short Reads Mapping for Exome Sequencing

Xueya Zhou, Suying Bao, Binbin Wang, Xuegong Zhang, and You-Qiang Song

 7. ­Profiling Short Tandem Repeats from Short Reads

Melissa Gymrek and Yaniv Erlich

 8. Exome Sequencing Analysis: A Guide to Disease Variant Detection

Ofer Isakov, Marie Perrone, and Noam Shomron

 9. Identifying RNA Editing Sites in miRNAs by Deep Sequencing

Shahar Alon and Eli Eisenberg

 10. Identifying Differential Alternative Splicing Events from RNA Sequencing Data using RNASeq-MATS

Juw Won Park, Collin Tokheim, Shihao Shen, and Yi Xing

 11. Optimizing Detection of Transcription Factor Binding Sites in ChIP-seq Experiments

Aleksi Kallio and Laura L. Elo

 12. Statistical Analysis of ChIP-seq Data with MOSAiCS

Guannan Sun, Dongjun Chung, Kun Liang, and Sündüz Keleș

 13. Detection of Reverse Transcriptase Termination Sites using cDNA Ligation and Massive Parallel Sequencing

Lukasz J. Kielpinski, Mette Boyd, Albin Sandelin, and Jeppe Vinther