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
