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.
SIPMeta help menu:
Usage:
with SIP output
simple <loopsFile> <RawData> <script> <sMetaPlot> <sImg> [options]
subtraction <loopsFile> <RawData1> <RawData2> <script> <sMetaPlot> <sImg> [options]
with .hic file
hic simple <loopsFile> <hicFile1> <outdir> <chrSizeFile> <JuicerBoxTools.jar> <script>
<sMetaPlot> <sImg> [options]
hic subtraction <loopsFile> <hicFile1> <hicFile2> <outdir1> <outdir2> <chrSizeFile>
<JuicerBoxTools.jar> <script> <sMetaPlot> <sImg> [options]
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).
-resMax TRUE or FALSE: default true, if false take the smaller resolution.
-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, --help print help.
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: pouletaxel@gmail.com OR jordan.rowley@unmc.edu