WARNING: We just noticed that the newest version of Juicer Tools (v1.22) interacts with SIPMeta in weird ways. Please use Juicer Tools v1.13 instead.

SIP

What is SIP?

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:

• Quick Start
• Parameter Selection Guide

Citing SIP

• View the Paper

Rowley MJ, Poulet A, Nichols MH, Bixler BJ, Sanborn AL, Brouhard EA, Hermetz K, Linsenbaum H, Csankovszki G, Lieberman Aiden E, Corces G. Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals. Genome Research 2020.

SIP help menu:

SIP_HiC run with java 8.

SIP is implemented in java and includes achoice between command line options or a graphical user interface (plop.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]

cool <mcoolFile> <chrSizeFile> <Output> <cooltoolsPath> <coolerPath> [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, res2 and res5
• -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 or --help print help

Command line eg:

java -jar SIP_HiC.jar processed inputDirectory pathToChromosome.size OutputDir [options]

java -jar SIP_HiC.jar hic pathTohicFile pathToChromosome.size OutputDir juicer_tools.jar [options]

java -jar SIP_HiC.jar cool pathTomcoolFile pathToChromosome.size Output cooltoolsPath coolerPath [options]

Authors:

• Axel Poulet: Department of Molecular, Cellular and Developmental Biology, Yale University, 165 Prospect St New Haven, CT 06511, USA. Contact: pouletaxel@gmail.com
• M. Jordan Rowley: Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center Omaha,NE 68198-5805. Contact: jordan.rowley@unmc.edu