Additional file 1 of Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering

Supplementary information. The supplementary information (pdf file) contains a very detailed description of the method implemented in Sierra Platinum and a description of Sierra Platinum (user interface and infrastructure) and its optimization. Furthermore, we present a very comprehensive benchmark of Sierra Platinum, i.e., a comparison to other peak-callers and peak-calling approaches for replicated ChIP-seq experiments for various conditions and a parameter benchmark for the parameters of Sierra Platinum. We provide derived parameter settings and guidelines for choosing the right parameters based on the quality measurements implemented in Sierra Platinum. The supplementary information contains also a more extensive comparison between the result of Sierra Platinum and MACS-CR on real data. (PDF 3000 kb)