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SPP

Wraps the SPP R package from http://compbio.med.harvard.edu/Supplements/ChIP-seq/ published in Kharchenko PK, Tolstorukov MY, Park PJ "Design and analysis of ChIP-seq experiments for DNA-binding proteins" Nat. Biotech. doi:10.1038/nbt.1508

Version 1.0
Bundle sequencing
Categories
Authors Lauri Lyly (lauri.lyly@helsinki.fi)
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Requires R ; SPP 1.10 (R-package)
Source files component.xml SPP.r
Usage Example with default values

Inputs

Name Type Mandatory Description
treatment BinaryFile Mandatory Sample CSV file, with fields: chromosome name, region middle position, strand (either 1 for forward or 2 for reverse)
control BinaryFile Mandatory Control CSV file with similar format as treatment file.

Outputs

Name Type Description
peaks CSV Called peaks regions ...

Parameters

Name Type Default Description
bin int 5 bin tags within the specified number of basepairs to speed up calculation
fdr float 0.01 Desired FDR.
srange_max int 500
srange_min int 50

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