1. Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks. 2. Identification of reads on the ChIP-enriched regions, which can be used for profiling and other quantitative analysis.
sh DIR/SICER.sh ["InputDir"] ["bed file"] ["control file"] ["OutputDir"] ["Species"] ["redundancy threshold"] ["window size (bp)"] ["fragment size"] ["effective genome fraction"] ["gap size (bp)"] ["FDR"]
Running SICER with a control library
Species: allowed species and genome versions are listed in GenomeData.py. You can add your own species and/or genome versions and relevant data there.
Redundancy Threshold: The number of copies of identical reads allowed in a library.
Window size: resolution of SICER algorithm. For histone modifications, one can use 200 bp
Fragment size: is for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75.
Effective genome fraction: Effective Genome as fraction of the genome size. It depends on read length.
Gap size: needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ….