SIP (Significant Interaction Peak caller) is a tool to identify and analyze loops that appear as high intensity signal in Hi-C maps. This program is written in java and can be run on Linux, Windows, or MAC systems and includes either command line options or a graphical user interface.
Follow the links below to get started:
SIP help menu:
#SIP Version 1 run with java 8
SIP is implemented in java and includes achoice between command line options or a graphical user
interface (gui) allowing for more general use. This method is intended as an alternative loop
caller especially for difficult to identify loops and works in conjunction with juicebox .hic files.
Usage:
hic <hicFile> <chrSizeFile> <Output> <juicerToolsPath> [options]
processed <Directory with processed data> <chrSizeFile> <Output> [options]
Parameters:
chrSizeFile: path to the chr size file, with the same name of the chr as in the hic file (i.e. chr1
does not match Chr1 or 1)
-res: resolution in bp (default 5000 bp)
-mat: matrix size to use for each chunk of the chromosome (default 2000 bins)
-d: diagonal size in bins, remove the maxima found at this size (eg: a size of 2 at 5000 bp resolution
removes all maxima detected at a distance inferior or equal to 10kb) (default 6 bins).
-g: Gaussian filter: smoothing factor to reduce noise during primary maxima detection (default 1.5)
-cpu: Number of CPU used for SIP processing (default 1)
-factor: Multiple resolutions can be specified using:
-factor 1: run only for the input res (default)
-factor 2: res and res*2
-factor 3: res and res*5
-factor 4: res, res*2 and res*5
-max: Maximum filter: increases the region of high intensity (default 2)
-min: Minimum filter: removes the isolated high value (default 2)
-sat: % of staturated pixel: enhances the contrast in the image (default 0.01)
-t Threshold for loops detection (default 2800 for hic)
-nbZero: number of zeros: number of pixels equal to zero that are allowed in the 24 pixels surrounding
the detected maxima (default 6)
-norm: <NONE/VC/VC_SQRT/KR> (default KR)
-del: true or false, whether not to delete tif files used for loop detection (default true)
-fdr: Empirical FDR value for filtering based on random sites (default 0.01)
-isDroso: default false, if true apply extra filter to help detect loops similar to those found in
D. mel cells
-h, --help print help
Command line eg:
java -jar SIP_HiC.jar processed inputDirectory pathToChromosome.size OutputDir .... paramaters
java -jar SIP_HiC.jar hic inputDirectory pathToChromosome.size OutputDir juicer_tools.jar
Authors:
Axel Poulet
Department of Molecular, Cellular and Developmental Biology
Yale University
165 Prospect St New Haven, CT 06511, USA
M. Jordan Rowley
Department of Genetics, Cell Biology and Anatomy,
University of Nebraska Medical Center
Omaha,NE 68198-5805
Contact: [email protected] OR [email protected]