See: A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq
Russell's pique software is available on github here: https://github.com/ryneches/pique.
The Pique software package processes ChIP-seq coverage data to predict protein-binding sites. Strand-specific coverage data are output as tracks for the Gaggle Genome Browser, and putative-binding sites (peaks) are output as ‘bookmark files’. (A) Screenshot of data browsing in the Gaggle Genome Browser. Green box outlines the navigation window for clicking through bookmarks of predicted binding sites. Details of each site can be displayed (inset). The Gaggle toolbar (shown with black arrow) can be used to broadcast selected data to other ‘geese’ in the gaggle package, programs such as R, cytoscape, BLAST or KEGG. (B) Schematic overview of bioinformatics workflow.