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.

SIPMeta

What is SIPMeta

SIPMeta is a tool to create both normal and bullseye transformed average metaplots of 2-D matrices, specifically Hi-C, HiChIP, or ChIA-PET data. This program is written in java with a helper python script and can be run on Linux, Windows, or MAC systems and includes either command line options or a graphical user interface.

Follow these links to get started.

• Installation & Quick Start

• Parameter Guide

If you use SIP or SIPMeta, please cite us.

• 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.

SIPMeta help menu:

1. with SIP output

java -jar SIPMeta.jar simple <loopsFile> <RawData> <script> <sMetaPlot> <sImg> [options]

java -jar SIPMeta.jar subtraction <loopsFile> <RawData1> <RawData2> <script> <sMetaPlot> <sImg> [options]

1. with .hic file

java -jar SIPMeta.jar hic simple <loopsFile> <hicFile1> <outdir> <chrSizeFile> <JuicerBoxTools.jar> <script> <sMetaPlot> <sImg> [options]

java -jar SIPMeta.jar hic subtraction <loopsFile> <hicFile1> <hicFile2> <outdir1> <outdir2> <chrSizeFile> <JuicerBoxTools.jar> <script> <sMetaPlot> <sImg> [options]

1. with .mcool file

java -jar SIPMeta.jar cool simple <loopsFile> <hicFile1> <outdir> <chrSizeFile> <cooler> <cooltools> <script> <sMetaPlot> <sImg> [options]

java -jar SIPMeta.jar cool subtraction <loopsFile> <hicFile1> <hicFile2> <outdir1> <outdir2> <chrSizeFile> <cooler> <cooltools> <script> <sMetaPlot> <sImg> [options]

More information for the command line mode here

Parameters:

• sMetaPlot: size of the desired metaplot (default 21 bins). Must be an odd number.
• sImg: size of the image analyzed by SIP. Corresponds to –mat option in SIP (default 2000 bins).
• 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).
• -norm: <NONE/VC/VC_SQRT/KR> only for hic option (default KR).
• -res: resolution in bp (default 5000 bp).
• -c: COLORSCHEME matplotlib_colors (Blues, BuGn, Greens, Purples, Reds, coolwarm, magma, inferno, spectral, viridis) default Reds. Can be any matplotlib color gradient.
• -z: Set this option to znorm each ring.
• -t: Threshold value tests the distance normalized value, all the value > T will be replaced by zero. Set high to avoid outliers skewing the average.
• -prefix: Prefix desired when naming the output files.
• -s: Set this option to trim edges to make a square plot but with Manhattan distances. (Not recommended as normal square plots are already created).
• -min: Min minimum value for color scale.
• -max: Max maximum value for color scale.
• -cpu: Number of CPU used for processing (default 1).
• -h or --help: print help.

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