Arrowhead（https://github.com/aidenlab/juicer/wiki/Arrowhead）
在以往的calling TAD 的軟件比較中，往往把arrowhead和其他軟件放入其中一同比較。但閱讀原文發(fā)現(xiàn)arrowhead 并非用來鑒定TAD，而是一些concat domain。這些contact domain 有些與CTCF的loop相對應(yīng)，而其他的更像是sub TAD（如下圖所示）。
讓我們再來看看原文的描述
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，讓我們看看腳本：
juicer_tools arrowhead sam1_chr10.hic ./contact_domains_list/
arrowhead 腳本非常簡單只需要輸入.hic 文件和輸出路徑即可。
arrowhead 結(jié)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
