从 .hic 文件提取数据

此功能由 Juicebox tools 的 dump 命令完成。
https://github.com/aidenlab/juicer/wiki/Data-Extraction

Arrowhead

Arrowhead is an algorithm for finding contact domains.

  1. arrowhead <HiC file> <output_file>

https://github.com/aidenlab/juicer/wiki/Arrowhead

生成一个12列的矩阵，每行包含以下信息

chromosome1 x1 x2 chromosome2 y1 y2 color corner_score Uvar Lvar Usign Lsign

Explanations of each field are as follows:
chromosome = the chromosome that the domain is located on
x1,x2/y1,y2 = the interval spanned by the domain (contact domains manifest as squares on the diagonal of a Hi-C matrix and as such: x1=y1, x2=y2)
color = the color that the feature will be rendered as if loaded in Juicebox
corner_score = the corner score, a score indicating the likelihood that a pixel is at the corner of a contact domain. Higher values indicate a greater likelihood of being at the corner of a domain
Uvar = the variance of the upper triangle
Lvar = the variance of the lower triangle
Usign = -1*(sum of the sign of the entries in the upper triangle)
Lsign = sum of the sign of the entries in the lower triangle

HiCCUPS

HiCCUPS is an algorithm for finding chromatin loops.
https://github.com/aidenlab/juicer/wiki/HiCCUPS
分为两个版本，gpu版本必须安装对应版本的CUDA。如果不能调用gpu的，可以使用cpu版本，加上参数--cpu。与gpu版本的区别是限制在对角线8M范围内进行搜索，所以会有遗漏，但是大部分都会找到（The vast majority of peaks (98%) reflected loops between loci that are <2 Mb apart）。

  1. hiccups [-m matrixSize] [-c chromosome(s)] [-r resolution(s)] 
  2.         <HiC file> <outputDirectory>

HiCCUPSDiff

HiCCUPS Diff allows you to find differential loops between loop lists.
https://github.com/aidenlab/juicer/wiki/HiCCUPSDiff

APA