1.DomainCaller 【任兵-densenty】
2.insulationscore 【dekker- densenty 】
https://github.com/dekkerlab/crane-nature-2015
# 安裝：ok
perl scripts/matrix2insulation.pl
perl?/home/shen/biosoft/crane-nature-2015-master/scripts/matrix2insulation.pl -i xxx.matrix?-is 500000 -ids 200000 -im mean -bmoe 3 -nt 0.1 -v
-b????????[] size (bp) of the insulation square
-v????? ? ?[]? ? ? ? FLAG, verbose mode
-ids? ? ? ?[]? ? ? ? insulation delta span (size (bp) of insulation delta window)
-im? ? ? ? ?[]? ? ? ? insulation mode (how to aggregrate signal within insulation square), mean,sum,median
-nt? ? ? ? ?[0.1]? ? ? noise threshold, minimum depth of valley
-bmoe? ? ? [3]? ? ? ? boundary margin of error (specified in number of BINS), added to each side of the boundary
軟件給的例子：
perl scripts/matrix2insulation.pl -i 10kb_chrX.matrix.gz -is 500000 -ids 200000 -im mean -bmoe 3 -nt 0.1 -v
perl scripts/matrix2insulation.pl -i 10kb_chrX.matrix.gz -is 500000 -ids 200000 -im mean -bmoe 3 -nt 0.1 -v
3.juicer：[.hic]
ref：https://github.com/aidenlab/juicer/blob/master/README.md
4.hicexplorer: 【.h5】
ref:?https://hicexplorer.readthedocs.io/en/latest/content/tools/hicFindTADs.html
5.tadtool：[可以對(duì)接hicpro輸出]
ref：https://github.com/vaquerizaslab/tadtool
pip intall tadtools
tadtools -h
Commands:
? ? plot? ? ? ? ? ? ? ? Main interactive TADtool plotting window
? ? tads? ? ? ? ? ? ? ? Call TADs with pre-defined parameters
? ? subset? ? ? ? ? ? ? Reduce a matrix to a smaller region.
my:
tadtool tads iced/50000/TU-2_50000_iced.matrix00_abs.bed 50000 0.005 tadtools_output.bed
tadtool plot iced/50000/TU-2_50000_iced.matrix raw/50000/TU-2_50000_abs.bed chr5:34000000-37000000
