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SICER (version 1.1)

ChIP-Seq Tag File:

ChIP-Seq Control File:

Fix off-by-one errors in output files:

SICER creates non-standard output files, this option will fix these coordinates

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:

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, ...

Statistic threshold value:

FDR (with control) or E-value (without control)

What it does

SICER first and foremost is a filtering tool. Its main functions are:

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.

View the original SICER documentation: http://home.gwu.edu/~wpeng/Software.htm.

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.

Citation If you use this tool in Galaxy, please cite Blankenberg D, et al. In preparation.