The analysis ready alignment files are then used to identify transcription factor binding sites, histone modifications, enriched motifs and other information typical to a ChIP-Seq experiment. We recommend researchers have at least one control sample for their treatments. This will give statistically better results compared to one without any controls.
There are many software available for ChIP-Seq analysis which have their own merits and downfalls (Excel spreadsheet). We use the currently popular tools HOMER and Macs2 for our pipeline. Some experiments produce clearly defined peaks of a 100–200 base-pairs as typified by transcription factors, e.g. ERα; others produce wider smears of a few to several hundreds of kilobases such as H3K27me3, and lastly, those that produce a mix of clearly defined peaks and wider smears such as RNA polymerase II. Most algorithms have been developed for analysis of clearly defined peaks, as these present the opportunity to determine nucleotide resolution of transcription factor binding and motif analysis. If you have any specific requests, please don't hesitate to contact us.
Regions called are annotated by default using HOMER and any regions called by other tools use snpEff. By default, regions lying with 30kb to the peak regions are annotated. This by no means pertains to all experiments and the parameters can be tweaked according to ones needs.