Command line usage - PouletAxel/SIPMeta GitHub Wiki

Command line

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

SIPMeta run with java 8

More information for the command line mode here

Usage:

  • 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]

Parameters:

  • sMetaPlot: size of the metaplot (default 21 bins). Must be an odd number

  • sImg: size of the image analysed by SIP (default 2000 bins)

  • chrSizeFile: path to the chromosome size file, with the same name of the chromosome as in the hic file

  • -norm: <NONE/VC/VC_SQRT/KR> only used with the hic option in juicer tools (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

  • -z: znorm each ring

  • -t: Threshold value tests the distance normalized value, all the value > T will be replaced by zero

  • -prefix: Prefix name to append to output files

  • -s: Trim edges to make a square plot with Manhattan distances

  • -min: min value for color scale

  • -max: max value for color scale

  • -cpu: Number of CPU used for processing (default 1)

  • -h, --help: print help

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