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Not able to see the specified normalizations (using -k) in the hic file after juicertools pre #347

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ashishjain1988 opened this issue Mar 13, 2024 · 0 comments
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@ashishjain1988
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I am generating the hic option using the juicertools version juicer_tools_1.22.01.jar. I am specifying the different normalizations in the option -k SCALE,KR but not able to see them in the final hic file on UCSC genome browser (seeing default ones NONE, VC,VC_SQRT,KR). Can you please help me with it?

Command: java -Xmx200000m -Djava.awt.headless=true -jar juicer_tools_1.22.01.jar pre -k SCALE,VC_SQRT D0_1_mapped.pairs D0_1_mapped-scale.hic hg38sizes.genome

Expected behavior
I should see the SCALE and VC_SQRT normalization options on UCSC genome browser

Desktop (please complete the following information):

  • OS: Linux
  • Juicertools jarversion: 1.22.01
  • jdk1.8.0_144

Additional context
Is there any way I can check the normalizations in the hic file?
I tried to use the other latest jars (v2.20.00) but getting the java.lang.ArrayIndexOutOfBoundsException: 3 exception.

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