SICER¶
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.
Details¶
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.
References¶
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
C. Zang, D.E. Schones, C. Zeng, K. Cui, K. Zhao and W. Peng.
Bioinformatics (2009) 25 (15): 1952-1958.