SIPMeta Quick Start - PouletAxel/SIPMeta GitHub Wiki

SIPMeta is a tool to create both normal and bullseye transformed average metaplots of 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.

1. Download the latest SIPMeta jar file (https://github.com/PouletAxel/SIPMeta/releases) with java 8 available on the server or computer. Because this is a jar file, MAC users may have to change the default security settings to enable the download.

2. Download the dependencies which will be used within SIPMeta later:

   1. The bullseye.py script also located at here.bullseye.py requires python 3. Additionally, the following python packages are required:
      1. matplotlib (pip install matplotlib)
      2. numpy (pip install numpy)
      3. scipy (pip install scipy)
   2. A loops file which can be generated with SIP: https://github.com/PouletAxel/SIP/releases
   3. 2-D data to summarize over the loops. Either: The output folder of SIP
   4. juicer toolbox: A program used to dump the data from the .hic file is available here:(https://github.com/aidenlab/juicer/wiki/Download), (Durand et al., 2016).
   5. cooler and cooltols: if you want use SIP with .mcool file you have to install cooler (https://github.com/mirnylab/cooler) (version >= 0.8.6) and cooltools (https://github.com/mirnylab/cooltools) (version >= 0.3.0) (Abdennur and Mirny, 2020). But those dependencies are not necessary if you are only running SIP with .hic file.
   • Chromosome size file: with each chromosome. The format is each line tab-delimited with:

chrName size

For the help menu: java -jar SIPMeta.jar -h

MetaSIP run with java 8

• 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]

• 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]

• 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

To launch the GUI : java -jar SIP_HiC.jar without any options. Alternately, you should be able to just double-click on the jar file if java file is configured correctly.

GUI usage info here

If you use SIP or SIPMeta, please cite us.

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.

Abdennur, N., Mirny, L.A., 2020. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 36, 311–316. https://doi.org/10.1093/bioinformatics/btz540

Durand, N.C., Shamim, M.S., Machol, I., Rao, S.S.P., Huntley, M.H., Lander, E.S., Aiden, E.L., 2016. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 3, 95–98. https://doi.org/10.1016/j.cels.2016.07.00