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?
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.
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):
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.