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Deep Sequencing Data Analysis

  • Book
  • © 2021

Overview

Editors:
  1. Noam Shomron

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

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2243)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Detecting Causal Variants in Mendelian Disorders Using Whole-Genome Sequencing

    • Abdul Rezzak Hamzeh, T. Daniel Andrews, Matt A. Field
    Pages 1-25

  3. Statistical Considerations on NGS Data for Inferring Copy Number Variations

    • Jie Chen
    Pages 27-58

  4. Applications of Community Detection Algorithms to Large Biological Datasets

    • Itamar Kanter, Gur Yaari, Tomer Kalisky
    Pages 59-80

  5. Processing and Analysis of RNA-seq Data from Public Resources

    • Yazeed Zoabi, Noam Shomron
    Pages 81-94

  6. Improved Analysis of High-Throughput Sequencing Data Using Small Universal k-Mer Hitting Sets

    • Yaron Orenstein
    Pages 95-105

  7. An Introduction to Whole-Metagenome Shotgun Sequencing Studies

    • Tyler A. Joseph, Itsik Pe’er
    Pages 107-122

  8. Microbiome Analysis Using 16S Amplicon Sequencing: From Samples to ASVs

    • Amnon Amir
    Pages 123-141

  9. RNA-Seq in Nonmodel Organisms

    • Vered Chalifa-Caspi
    Pages 143-167

  10. Deep Learning Applied on Next Generation Sequencing Data Analysis

    • Artem Danilevsky, Noam Shomron
    Pages 169-182

  11. Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq

    • Georgi K. Marinov, Zohar Shipony
    Pages 183-226

  12. Genome-Wide Noninvasive Prenatal Diagnosis of SNPs and Indels

    • Tom Rabinowitz, Noam Shomron
    Pages 227-248

  13. Genome-Wide Noninvasive Prenatal Diagnosis of De Novo Mutations

    • Ravit Peretz-Machluf, Tom Rabinowitz, Noam Shomron
    Pages 249-269

  14. Accurate Imputation of Untyped Variants from Deep Sequencing Data

    • Davoud Torkamaneh, François Belzile
    Pages 271-281

  15. Multiregion Sequence Analysis to Predict Intratumor Heterogeneity and Clonal Evolution

    • Soyeon Ahn, Haiyan Huang
    Pages 283-296

  16. Overcoming Interpretability in Deep Learning Cancer Classification

    • Yue Yang (Alan) Teo, Artem Danilevsky, Noam Shomron
    Pages 297-309

  17. Single-Cell Transcriptome Profiling

    • Guy Shapira, Noam Shomron
    Pages 311-325

  18. Biological Perspectives of RNA-Sequencing Experimental Design

    • Metsada Pasmanik-Chor
    Pages 327-337

  19. Analysis of microRNA Regulation in Single Cells

    • Wendao Liu, Noam Shomron
    Pages 339-354

  20. DNA Data Collection and Analysis in the Forensic Arena

    • Sydnie Grabell, Noam Shomron
    Pages 355-368
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Keywords

About this book

This second edition provides new and updated chapters from expert researchers in the field detailing methods used to study the multi-facet deep sequencing data field. Chapters guide readers through techniques for processing RNA-seq data, microbiome analysis, deep learning methodologies, 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 the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 Authoritative and cutting-edge, Deep Sequencing Data Analysis: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

Editors and Affiliations

  • Sackler 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/10.1007/978-1-0716-1103-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1102-9Published: 20 February 2021

  • Softcover ISBN: 978-1-0716-1105-0Published: 20 February 2022

  • eBook ISBN: 978-1-0716-1103-6Published: 19 February 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: X, 374

  • Number of Illustrations: 11 b/w illustrations, 81 illustrations in colour

  • Topics: Genetics and Genomics, Bioinformatics

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