TSSAR: Transcription Start Site Annotation Regime Web Service

Introduction to the TSSAR Client

A single NGS run typically produces huge amount of data. It is not easy to handle gigabyte files locally and an Internet transfer using standard protocols such as http is almost impossible. To circumvent this problem TSSAR uses a platform independent java client that boils dRNA-seq data down to the necessary information and makes thereby an Internet file transfer possible.

Method

Standard Java and three external, i.e. httpcomponents, picard and xz, libraries are used to provide an user friendly graphical user interface which is used to pre-process dRNA-seq data locally on the user's computer. The interface asks for general, e.g. email address, and experiment specific, e.g. NCBI ID and genome size, information. It offers the possibility to upload a single experiment which consists of mapped reads of a TEX treated and an untreated sequencing library or up to five such experiments for one species at once. When all information is given the client locally processes all files and subsequently submits them to the TSSAR Web Server. The complete client-server communication is encapsulated in the Java client which is most convenient for the user. The Web Server forwards the data to the TSSAR Statistics component of the TSSAR pipeline and finally displays the results.