May 16, 2014

SraTailor: GUI software for visualizing high-throughput sequence read archives

BioRxiv : the Preprint Server for Biology
Shinya OkiChikara Meno

Abstract

Raw high-throughput sequence data are deposited in public databases as SRAs (Sequence Read Archives) and are publically available to every researcher. However, in order to graphically visualize the sequence data of interest, the corresponding SRAs must be downloaded and converted into BigWig format through complicated command-line processing. This task requires users to possess skill with script languages and sequence data processing, a requirement that prevents a wide range of biologists from exploiting SRAs. To address these challenges, we developed SraTailor, a GUI (Graphical User Interface) software package that automatically converts an SRA into a BigWig-formatted file. Simplicity of use is one of the most notable features of SraTailor: entering an accession number of an SRA and clicking the mouse are the only steps required in order to obtain BigWig-formatted files and to graphically visualize the extents of reads at given loci. SraTailor is also able to make peak calls and files of other formats, and the software also accepts various command-line-like options. Therefore, this software makes SRAs fully exploitable by a wide range of biologists. SraTailor is freely available at <http://www.dev.med.kyushu-u.ac.jp/sra_tailor/>.

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Mentioned in this Paper

Computer Software
Steroid receptor RNA activator
CYFIP1 protein, human
High Throughput Analysis
Biologist (General)
Operator Regions, Genetic
Script
Laboratory mice
Cell Line, Tumor
BAT Loci

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