START : a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries

Abstract

A genomic signal track is a set of genomic intervals associated with values of various types, such as measurements from high-throughput experiments. Analysis of signal tracks requires complex computational methods, which often make the analysts focus too much on the detailed computational steps rather than on their biological questions. This thesis presents Signal Track Analytical Research Tool (START) and Signal Track Query Language (STQL) for easy analysis of signal tracks. STQL is an SQL-like declarative language, which means one only specifies what computations need to be done but not how these computations are to be carried out. STQL provides a rich set of constructs for manipulating genomic intervals and their values. To run STQL queries, we have developed the Signal Track Analytical Research Tool (START), a MapReduce-based system that includes a Web-based user interface and a back-end execution system. By running some typical analyses tasks, we show that the START+STQL solution is usually the simplest, and the parallel execution achieves significant speed-up with large data files.