Workflow within the Cistrome analysis platform. Cistrome functions can be divided into three categories: data preprocessing, gene expression and integrative analysis. A general workflow using Cistrome is to upload datasets, preprocess them using peak calling tools to generate peak locations in BED format and signal profiles in WIGGLE format, upload gene expression data to produce specific gene lists, and then use various integrative analysis tools to generate figures and reports. The bottom figure shows the web interface of the Cistrome platform based on the Galaxy framework. The left panel shows available tools, the middle panel shows messages, tool options, or result details, and the right panel shows the datasets organized in the user's history, including datasets that have been or are being processed (in green and yellow, respectively), or waiting in the queue (in gray). CEAS,; DC, Data Collection module; GEO, Gene Expression Omnibus; NPS, Nucleosome Positioning from Sequencing; TF, transcription factor.
Liu et al. Genome Biology 2011 12:R83 doi:10.1186/gb-2011-12-8-r83