juicer

ref： annotation ： https://github.com/aidenlab/juicer/wiki/Feature-Annotation

eigenvector <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr> <BP/FRAG> <binsize> [outfile]

example：

java -jar /media/shen/*/sun/biosoft/juicer_tools.jar eigenvector VC xxx.hic X BP 5000 juicer.pca.eigen.txt

my:

java -jar /media/shen/*/sun/biosoft/juicer_tools.jar eigenvector VC TU-2.allValidPairs.hic chr19 BP 500000 juicer.pca.eigen.txt

arrowhead [-c chromosome(s)] [-m matrix size] [-r resolution]

[-k normalization (NONE/VC/VC_SQRT/KR)] <HiC file>

<output_file> [feature_list] [control_list]

example：

java -jar /media/shen/*/sun/biosoft/juicer_tools.jar  arrowhead  xxx.hic contact_domains_list -c chr19 -m 2000 -r 50000 -k KR

my:

java -jar /media/shen/*/sun/biosoft/juicer_tools.jar arrowhead TU-2.allValidPairs.hic contact_domains_list -c chr19 -m 2000 -r 50000 -k KR --ignore_sparsity