1.DomainCaller 【任兵-densenty】

http://yuelab.org/hi-c/

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