Jucer-arrowhead call TAD?

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

在以往的calling TAD 的软件比较中，往往把arrowhead和其他软件放入其中一同比较。但阅读原文发现arrowhead 并非用来鉴定TAD，而是一些concat domain。这些contact domain 有些与CTCF的loop相对应，而其他的更像是sub TAD（如下图所示）。

让我们再来看看原文的描述:
In our new, higher resolution maps (200- to 1,000-fold more contacts), we observe many small squares of enhanced contact frequency that tile the diagonal of each contact matrix (Figure 2A). We used the Arrowhead algorithm (see Experimental Procedures) to annotate these contact domains genome-wide. The observed domains ranged in size from 40 kb to 3 Mb (median size 185 kb). As with megadomains, there is an abrupt drop in contact frequency (33%) for pairs of loci on opposite sides of the domain boundary (Figure S2G). Contact domains are often preserved across cell types (Figures S3A and S3B).

看完了arrowhead的描述，让我们看看脚本：

juicer_tools  arrowhead   sam1_chr10.hic   ./contact_domains_list/

arrowhead 脚本非常简单只需要输入.hic 文件和输出路径即可。
arrowhead 结果文件：

chr1    x1  x2  chr2    y1  y2  name    score   strand1 strand2 color   score   uVarScore   lVarScore   upSign  loSign
10  52700000    53985000    10  52700000    53985000    .   .   .   .   255,255,0   0.41747454097878034 0.41970000160383647 0.409477935545163   0.43657232137491736 0.48025959978366684
10  9365000 11530000    10  9365000 11530000    .   .   .   .   255,255,0   0.36420329490041414 0.41362580689849504 0.3894973896850802  0.401325150247403840.4640574231773875
10  15455000    16850000    10  15455000    16850000    .   .   .   .   255,255,0   0.5489743298631723  0.40563766266026124 0.35380396518498225 0.476734693877551   0.5882142857142857
10  125745000   126090000   10  125745000   126090000   .   .   .   .   255,255,0   0.6609615269302085  0.36916154242309135 0.3879633742571127  0.5828571428571429  0.5542857142857143
10  100215000   101135000   10  100215000   101135000   .   .   .   .   255,255,0   0.755689961290954   0.31256138469800887 0.3220336759786886  0.5375175315568023  0.5839177185600748
10  6450000 7525000 10  6450000 7525000 .   .   .   .   255,255,0   0.8279503126182577  0.3265788783197742  0.30777127122093495 0.5869341563786008  0.6081104252400549
10  15920000    16830000    10  15920000    16830000    .   .   .   .   255,255,0   0.9782706809375372  0.30248721264752976 0.24512848132657034 0.5738174868609651  0.7514333492594362
10  96370000    96870000    10  96370000    96870000    .   .   .   .   255,255,0   0.900385516954811   0.24702025315833226 0.28021307721486366 0.7490196078431373  0.4541176470588235
10  50785000    51125000    10  50785000    51125000    .   .   .   .   255,255,0   0.9495222201309195  0.3058902380876848  0.19212681234041373 0.6067226890756302  0.7605042016806722

每列代表如下:

• 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

作者：XuningFan
链接：https://www.jianshu.com/p/800d671e70fa
来源：简书
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