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Deep Sequencing Data Analysis

  • Book
  • © 2013

Overview

Editors:
  1. Noam Shomron

    1. , Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

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  • Includes cutting-edge methods and protocols in the MiMB standard format
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1038)

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Table of contents (13 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. An Introduction to High-Throughput Sequencing Experiments: Design and Bioinformatics Analysis

    • Rachelly Normand, Itai Yanai
    Pages 1-26

  3. Compressing Resequencing Data with GReEn

    • Armando J. Pinho, Diogo Pratas, Sara P. Garcia
    Pages 27-37

  4. On the Accuracy of Short Read Mapping

    • Peter Menzel, Jes Frellsen, Mireya Plass, Simon H. Rasmussen, Anders Krogh
    Pages 39-59

  5. Statistical Modeling of Coverage in High-Throughput Data

    • David Golan, Saharon Rosset
    Pages 61-79

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

    • Nitzan Kol, Noam Shomron
    Pages 81-91

  7. Short Read Mapping for Exome Sequencing

    • Xueya Zhou, Suying Bao, Binbin Wang, Xuegong Zhang, You-Qiang Song
    Pages 93-111

  8. Profiling Short Tandem Repeats from Short Reads

    • Melissa Gymrek, Yaniv Erlich
    Pages 113-135

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

    • Ofer Isakov, Marie Perrone, Noam Shomron
    Pages 137-158

  10. Identifying RNA Editing Sites in miRNAs by Deep Sequencing

    • Shahar Alon, Eli Eisenberg
    Pages 159-170

  11. Identifying Differential Alternative Splicing Events from RNA Sequencing Data Using RNASeq-MATS

    • Juw Won Park, Collin Tokheim, Shihao Shen, Yi Xing
    Pages 171-179

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

    • Aleksi Kallio, Laura L. Elo
    Pages 181-191

  13. Statistical Analysis of ChIP-seq Data with MOSAiCS

    • Guannan Sun, Dongjun Chung, Kun Liang, Sündüz Keleş
    Pages 193-212

  14. Detection of Reverse Transcriptase Termination Sites Using cDNA Ligation and Massive Parallel Sequencing

    • Lukasz J. Kielpinski, Mette Boyd, Albin Sandelin, Jeppe Vinther
    Pages 213-231

  15. Back Matter

    Pages 233-234
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Keywords

About this book

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.

Editors and Affiliations

  • , Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

    Noam Shomron

Bibliographic Information

  • Book Title: Deep Sequencing Data Analysis

  • Editors: Noam Shomron

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-514-9

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2013

  • Hardcover ISBN: 978-1-62703-513-2Published: 20 July 2013

  • Softcover ISBN: 978-1-4939-6027-9Published: 23 August 2016

  • eBook ISBN: 978-1-62703-514-9Published: 20 July 2013

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 234

  • Number of Illustrations: 38 b/w illustrations, 43 illustrations in colour

  • Topics: Bioinformatics, Human Genetics

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