START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries
Abstract Background 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 comp...
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doaj-57b609a486fd4677a99168b5154b364e2020-11-25T02:34:42ZengBMCBMC Genomics1471-21642017-09-0118111810.1186/s12864-017-4071-1START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queriesXinjie Zhu0Qiang Zhang1Eric Dun Ho2Ken Hung-On Yu3Chris Liu4Tim H. Huang5Alfred Sze-Lok Cheng6Ben Kao7Eric Lo8Kevin Y. Yip9Department of Computer Science, The University of Hong KongSchool of Computing, Hong Kong Polytechnic UniversityDepartment of Computer Science and Engineering, The Chinese University of Hong KongDepartment of Computer Science and Engineering, The Chinese University of Hong KongDepartment of Computer Science and Engineering, The Chinese University of Hong KongDepartment of Molecular Medicine, University of Texas Health Science Center at San AntonioSchool of Biomedical Sciences, The Chinese University of Hong KongDepartment of Computer Science, The University of Hong KongDepartment of Computer Science and Engineering, The Chinese University of Hong KongDepartment of Computer Science and Engineering, The Chinese University of Hong KongAbstract Background 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. Results Here we propose Signal Track Query Language (STQL) for simple analysis of signal tracks. It is a Structured Query Language (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, http://yiplab.cse.cuhk.edu.hk/start/ ), a system that includes a Web-based user interface and a back-end execution system. The user interface helps users select data from our database of around 10,000 commonly-used public signal tracks, manage their own tracks, and construct, store and share STQL queries. The back-end system automatically translates STQL queries into optimized low-level programs and runs them on a computer cluster in parallel. We use STQL to perform 14 representative analytical tasks. By repeating these analyses using bedtools, Galaxy and custom Python scripts, we show that the STQL solution is usually the simplest, and the parallel execution achieves significant speed-up with large data files. Finally, we describe how a biologist with minimal formal training in computer programming self-learned STQL to analyze DNA methylation data we produced from 60 pairs of hepatocellular carcinoma (HCC) samples. Conclusions Overall, STQL and START provide a generic way for analyzing a large number of genomic signal tracks in parallel easily.http://link.springer.com/article/10.1186/s12864-017-4071-1Human genomicsSignal tracksData analysis |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xinjie Zhu Qiang Zhang Eric Dun Ho Ken Hung-On Yu Chris Liu Tim H. Huang Alfred Sze-Lok Cheng Ben Kao Eric Lo Kevin Y. Yip |
spellingShingle |
Xinjie Zhu Qiang Zhang Eric Dun Ho Ken Hung-On Yu Chris Liu Tim H. Huang Alfred Sze-Lok Cheng Ben Kao Eric Lo Kevin Y. Yip START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries BMC Genomics Human genomics Signal tracks Data analysis |
author_facet |
Xinjie Zhu Qiang Zhang Eric Dun Ho Ken Hung-On Yu Chris Liu Tim H. Huang Alfred Sze-Lok Cheng Ben Kao Eric Lo Kevin Y. Yip |
author_sort |
Xinjie Zhu |
title |
START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries |
title_short |
START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries |
title_full |
START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries |
title_fullStr |
START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries |
title_full_unstemmed |
START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries |
title_sort |
start: a system for flexible analysis of hundreds of genomic signal tracks in few lines of sql-like queries |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2017-09-01 |
description |
Abstract Background 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. Results Here we propose Signal Track Query Language (STQL) for simple analysis of signal tracks. It is a Structured Query Language (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, http://yiplab.cse.cuhk.edu.hk/start/ ), a system that includes a Web-based user interface and a back-end execution system. The user interface helps users select data from our database of around 10,000 commonly-used public signal tracks, manage their own tracks, and construct, store and share STQL queries. The back-end system automatically translates STQL queries into optimized low-level programs and runs them on a computer cluster in parallel. We use STQL to perform 14 representative analytical tasks. By repeating these analyses using bedtools, Galaxy and custom Python scripts, we show that the STQL solution is usually the simplest, and the parallel execution achieves significant speed-up with large data files. Finally, we describe how a biologist with minimal formal training in computer programming self-learned STQL to analyze DNA methylation data we produced from 60 pairs of hepatocellular carcinoma (HCC) samples. Conclusions Overall, STQL and START provide a generic way for analyzing a large number of genomic signal tracks in parallel easily. |
topic |
Human genomics Signal tracks Data analysis |
url |
http://link.springer.com/article/10.1186/s12864-017-4071-1 |
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