TAD方法
1.DomainCaller 【任兵-densenty】
2.insulationscore 【dekker- densenty 】
https://github.com/dekkerlab/crane-nature-2015
# 安装：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
软件给的例子：
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：[可以对接hicpro输出]
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
