1 Introduction ................................................. 1
Naiara Rodríguez-Ezpeleta and Ana M. Aransay
2 Overview of Sequencing Technology Platforms ................. 11
Samuel Myllykangas, Jason Buenrostro, and Hanlee P. Ji
3 Applications of High-Throughput Sequencing .................. 27
Rodrigo Goya, Irmtraud M. Meyer, and Marco A. Marra
4 Computational Infrastructure and Basic Data Analysis for
High-Throughput Sequencing .................................. 55
David Sexton
5 Base-Calling for Bioinformaticians .......................... 67
Mona A. Sheikh and Yaniv Erlich
6 De Novo Short-Read Assembly ................................. 85
Douglas W. Bryant Jr. and Todd C. Mockler
7 Short-Read Mapping ......................................... 107
Paolo Ribeca
8 DNA-Protein Interaction Analysis (ChIP-Seq) ................ 127
Geetu Tuteja
9 Generation and Analysis of Genome-Wide DNA Methylation
Maps ....................................................... 151
Martin Kerick, Axel Fischer, and Michal-Ruth Schweiger
10 Differential Expression for RNA Sequencing (RNA-Seq)
Data: Mapping, Summarization, Statistical Analysis,
and Experimental Design .................................... 169
Matthew D. Young, Davis J. McCarthy, Matthew
J. Wakefield, Gordon K. Smyth, Alicia Oshlack, and
Mark D. Robinson
11 MicroRNA Expression Profiling and Discovery ................ 191
Michael Hackenberg
12 Dissecting Splicing Regulatory Network by Integrative
Analysis of CLIP-Seq Data .................................. 209
Michael Q. Zhang
13 Analysis of Metagenomics Data .............................. 219
Elizabeth M. Glass and Folker Meyer
14 High-Throughput Sequencing Data Analysis Software:
Current State and Future Developments ...................... 231
Konrad Paszkiewicz and David J. Studholme
Index ......................................................... 249
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