We have developed a query language called the Signal Track Query Language (STQL). It is an SQL-like declarative language for analyzing genomic signal tracks. We have also developed a web site called Signal Track Analytical Research Tool (START, http://yiplab.cse.cuhk.edu.hk/start/) for executing STQL queries involving both commonly-used signal tracks stored in our database and users’ own signal tracks. Sample STQL queries are provided on START for various representative analytical tasks.
The language specification of STQL is available at https://github.com/stql/start/blob/master/for-download/stql.pdf, while detailed documentation of START can be found on our GitHub page (https://github.com/stql/start/wiki).
You are welcome to try it out. Please let us know (emailing kevinyip@cse.cuhk.edu.hk) if you have any suggestions or questions.
Interesting. Should be useful for drill-down analyses of chip-seq peaks when bedtools don't suffice.