An Integrated Data Analysis Suite and Programming ... - TOBIAS-lib

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CONTENTS
2.6 A Parallelization Front-End for Short Read Alignment Tools . . . . . . . . . . . 43
2.7 Robust Detection of ChIP-Seq Enrichment . . . . . . . . . . . . . . . . . . . . . . 45
2.7.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
2.7.2 Correcting for Duplicated Sequences . . . . . . . . . . . . . . . . . . . . . 45
2.7.3 Detection Phase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
2.7.4 Recognition of Read Mapping Artifacts . . . . . . . . . . . . . . . . . . . 47
2.7.5 Ranking and Assessment of Peak Signicance . . . . . . . . . . . . . . . . 49
2.7.6 Experimental Relevance of Peak Signicance . . . . . . . . . . . . . . . . 51
2.8 Visualization of Sequencing Read and Alignment Data . . . . . . . . . . . . . . . 52
2.8.1 Gathering Run Quality and Sequence Composition Statistics . . . . . . . 52
2.8.2 Visualization of Read Mapping Data . . . . . . . . . . . . . . . . . . . . . 55
2.8.3 Visualization of Local or Genome-Scale Depth of Coverage . . . . . . . . 56
2.8.4 Quantile Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
3 A C++ Framework for High-Throughput DNA Sequencing 61
3.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
3.2 A Modular Signal-Slot Processing Framework . . . . . . . . . . . . . . . . . . . . 64
3.2.1 Reader and Writer Concepts . . . . . . . . . . . . . . . . . . . . . . . . . 64
3.2.2 Denition of Processing Network Topology . . . . . . . . . . . . . . . . . 64
3.2.3 Module Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
3.2.4 In-Place Data Manipulation . . . . . . . . . . . . . . . . . . . . . . . . . . 69
3.3 A Simplied Parallelization Interface . . . . . . . . . . . . . . . . . . . . . . . . . 71
3.3.1 Parallelization Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
3.3.2 Parallel Pipeline Architecture . . . . . . . . . . . . . . . . . . . . . . . . . 73
4 Closing Remarks 77
Bibliography 81