A/B compartments

[nservant]

Available for A/B comparments calling ;

FANC

fanc DATA.cool output.ab -d compartments.fanc

HiTC

call_compartments.r --matrix ${mat} --bed ${bed}                                                                                                                                                           

cootools

cooltools genome gc BIN_PATH FASTA_PATH
cooltools call-compartments results/contact_maps/cool/SRR400264_01_1000000.cool -o cooltools_AB --bigwig --reference-track GC_FILE

HiCExplorer

hicPCA --matrix DATA.h5 --outputFileName hicexplorer_ABcompartments

[nservant]

deeptools/HiCExplorer#346

[nservant]

cooltools genome binnify chrom_hg19.sizes 100000 > bins.txt
cooltools genome gc bins.txt hg19.fa > gc.txt
cooltools call-compartments --reference-track gc.txt --contact-type cis -o test_comp SRR400264_1000000_norm.cool

[nservant]

Need to update cooltools to v0.4.0 and use

cooltools genome binnify --all-names ${chrsize} ${res} > genome_bins.txt

open2c/cooltools#237

[nservant]

done in v.1.3.0