SICER first and foremost is a filtering tool. Its main functions are:
- Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks.
- Identification of reads on the ChIP-enriched regions, which can be used for profiling and other quantitative analysis.
By default, SICER creates files that do not conform to standards (e.g. BED files are closed, not half-open). This could have implications for downstream analysis. To force the output of SICER to be formatted properly to standard file formats, check the “Fix off-by-one errors in output files” option.