Abstract
High-throughput sequencing has revolutionized biology by enhancing our ability to perform genome-wide studies. However, due to lack of bioinformatics expertise, modern technologies are still beyond the capabilities of many laboratories. Herein, we present the BioWardrobe platform, which allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-friendly web interface, without the need for programming expertise. Predefined pipelines allow users to download data, visualize results on a genome browser, calculate RPKMs (reads per kilobase per million) and identify peaks. Advanced capabilities include differential gene expression and binding analysis, and creation of average tag -density profiles and heatmaps. BioWardrobe can be found at http://biowardrobe.com.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0720-3) contains supplementary material, which is available to authorized users.
Highlights
The recent proliferation of next-generation sequencing (NGS)-based methods for analysis of gene expression, chromatin structure and protein–DNA interactions has opened new horizons for molecular biology
The pipelines are selected on the basis of biologist-friendly experimental parameters (e.g., RNA/Chromatin immunoprecipitation (ChIP)-Seq, paired/ single, genome, stranded/unstranded, antibody) and combine the tools developed by ourselves and by others (e.g., Bowtie [8], STAR [15], FASTX [16] and MACS2 [17]) with wrappers that enhance the output of original software by offering additional information, provide experimentally meaningful quality controls, and display results within a web interface
The dataset included Helicos RNA sequencing (RNA-Seq) performed in triplicates for both resting naïve T helper (Thn) cells and cells differentiated in T helper type 1 (Th1) conditions for 72 hours (Th1 cells) and Histone 3 lysine trimethlation (H3K4me3) ChIP-Seq data of Th1 cells
Summary
The recent proliferation of next-generation sequencing (NGS)-based methods for analysis of gene expression, chromatin structure and protein–DNA interactions has opened new horizons for molecular biology. Even when processed data files (e.g., gene expression values) are available, direct comparison between datasets is ill-advised because different laboratories use different pipelines (or different software versions). BioWardrobe features include download of raw data from core facilities or online databases (e.g., GEO), read mapping and data display on a local instance of the University of California, Santa Cruz (UCSC) genome browser [14], quality control and both basic and advanced data analysis (Fig. 1a).
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