chia pet2 output格式（chr10的部分）
ChIA-PET2 -g genomeindex -b bedtoolsgenome -f fq1 -r fq2 -A linkerA -B linkerB -o OUTdir -n prefixname
参数说明：
-g bwa的基因组索引文件
-b 为bedtools提供的染色体大小文件（UCSC上下载）
-f，-r 输入的两个fastq（.gz）文件
-A，-B 两个linker序列，默认为GTTGGATAAG 和 GTTGGAATGT
-o 输出目录，默认为output
-n 输出文件的前缀名
可以通过-t设置线程数，其他可选参数可以看ChIA-PET2的GItHub主页。
chr1 249250621
chr2 243199373
chr3 198022430
chr4 191154276
chr5 180915260
chr6 171115067
chr7 159138663
chrX 155270560
chr8 146364022
chr9 141213431
chr10 135534747
chr11 135006516
chr12 133851895
chr13 115169878
chr14 107349540
chr15 102531392
chr16 90354753
chr17 81195210
chr18 78077248
chr20 63025520
chrY 59373566
chr19 59128983
chr22 51304566
chr21 48129895
chia pet2 output后得到intra.bedpe 和inter.bedpe的文件
在处理经过某种处理后的到的格式（chr10的部分）
bin183571|ce10|chr1:0-10000 bin183572|ce10|chr1:10000-20000 bin183573|ce10|chr1:20000-30000 bin183574|ce10|chr1:30000-40000 bin183575|ce10|chr1:40000-50000 bin183576|ce10|chr1:50000-60000 bin183577|ce10|chr1:60000-70000 bin183578|ce10|chr1:70000-80000 bin183579|ce10|chr1:80000-90000 bin183580|ce10|chr1:90000-100000 bin183581|ce10|chr1:100000-110000 bin183582|ce10|chr1:110000-120000 bin183583|ce10|chr1:120000-130000 bin183584|ce10|chr1:130000-140000 bin183585|ce10|chr1:140000-150000 bin183586|ce10|chr1:150000-160000 bin183587|ce10|chr1:160000-170000 bin183588|ce10|chr1:170000-180000 bin183589|ce10|chr1:180000-190000 bin183590|ce10|chr1:190000-200000 bin183591|ce10|chr1:200000-210000 bin183592|ce10|chr1:210000-220000 bin183593|ce10|chr1:220000-230000 bin183594|ce10|chr1:230000-240000 bin183595|ce10|chr1:240000-250000 bin183596|ce10|chr1:250000-260000 bin183597|ce10|chr1:260000-270000 bin183598|ce10|chr1:270000-280000 bin183599|ce10|chr1:280000-290000 bin183600|ce10|chr1:290000-300000 bin183601|ce10|chr1:300000-310000 bin183602|ce10|chr1:310000-320000 bin183603|ce10|chr1:320000-330000 bin183604|ce10|chr1:330000-340000 bin183605|ce10|chr1:340000-350000 bin183606|ce10|chr1:350000-360000 bin183607|ce10|chr1:360000-370000 bin183608|ce10|chr1:370000-380000 bin183609|ce10|chr1:380000-390000 bin183610|ce10|chr1:390000-400000 bin183611|ce10|chr1:400000-410000 bin183612|ce10|chr1:410000-420000 bin183613|ce10|chr1:420000-430000 bin183614|ce10|chr1:430000-440000 bin183615|ce10|chr1:440000-450000 bin183616|ce10|chr1:450000-460000 bin183617|ce10|chr1:460000-470000 bin183618|ce10|chr1:470000-480000 bin183619|ce10|chr1:480000-490000 bin183620|ce10|chr1:490000-500000 bin183621|ce10|chr1:500000-510000 bin183622|ce10|chr1:510000-520000 bin183623|ce10|chr1:520000-530000 bin183624|ce10|chr1:530000-540000 bin183625|ce10|chr1:540000-550000 bin183626|ce10|chr1:550000-560000 bin183627|ce10|chr1:560000-570000 bin183628|ce10|chr1:570000-580000 bin183629|ce10|chr1:580000-590000 bin183630|ce10|chr1:590000-600000 bin183631|ce10|chr1:600000-610000 bin183632|ce10|chr1:610000-620000 bin183633|ce10|chr1:620000-630000 bin183634|ce10|chr1:630000-640000 bin183635|ce10|chr1:640000-650000 bin183636|ce10|chr1:650000-660000 bin183637|ce10|chr1:660000-670000 bin183638|ce10|chr1:670000-680000 bin183639|ce10|chr1:680000-690000 bin183640|ce10|chr1:690000-700000 bin183641|ce10|chr1:700000-710000 bin183642|ce10|chr1:710000-720000 bin183643|ce10|chr1:720000-730000 bin183644|ce10|chr1:730000-740000 bin183645|ce10|chr1:740000-750000 bin183646|ce10|chr1:750000-760000 bin183647|ce10|chr1:760000-770000 bin183648|ce10|chr1:770000-780000 bin183649|ce10|chr1:780000-790000 bin183650|ce10|chr1:790000-800000 bin183651|ce10|chr1:800000-810000 bin183652|ce10|chr1:810000-820000 bin183653|ce10|chr1:820000-830000 bin183654|ce10|chr1:830000-840000 bin183655|ce10|chr1:840000-850000 bin183656|ce10|chr1:850000-860000 bin183657|ce10|chr1:860000-870000 bin183658|ce10|chr1:870000-880000 bin183659|ce10|chr1:880000-890000 bin183660|ce10|chr1:890000-900000 bin183661|ce10|chr1:900000-910000 bin183662|ce10|chr1:910000-920000 bin183663|ce10|chr1:920000-930000 bin183664|ce10|chr1:930000-940000 bin183665|ce10|chr1:940000-950000 bin183666|ce10|chr1:950000-960000 bin183667|ce10|chr1:960000-970000 bin183668|ce10|chr1:970000-980000 bin183669|ce10|chr1:980000-990000
。。。。。
chrX的部分
bin139284|ce10|chr1:0-10000 bin139285|ce10|chr1:10000-20000 bin139286|ce10|chr1:20000-30000 bin139287|ce10|chr1:30000-40000 bin139288|ce10|chr1:40000-50000 bin139289|ce10|chr1:50000-60000 bin139290|ce10|chr1:60000-70000 bin139291|ce10|chr1:70000-80000 bin139292|ce10|chr1:80000-90000 bin139293|ce10|chr1:90000-100000 bin139294|ce10|chr1:100000-110000 bin139295|ce10|chr1:110000-120000 bin139296|ce10|chr1:120000-130000 bin139297|ce10|chr1:130000-140000 bin139298|ce10|chr1:140000-150000 bin139299|ce10|chr1:150000-160000 bin139300|ce10|chr1:160000-170000 bin139301|ce10|chr1:170000-180000 bin139302|ce10|chr1:180000-190000 bin139303|ce10|chr1:190000-200000 bin139304|ce10|chr1:200000-210000 bin139305|ce10|chr1:210000-220000 bin139306|ce10|chr1:220000-230000 bin139307|ce10|chr1:230000-240000 bin139308|ce10|chr1:240000-250000 bin139309|ce10|chr1:250000-260000 bin139310|ce10|chr1:260000-270000 bin139311|ce10|chr1:270000-280000 bin139312|ce10|chr1:280000-290000 bin139313|ce10|chr1:290000-300000 bin139314|ce10|chr1:300000-310000 bin139315|ce10|chr1:310000-320000 bin139316|ce10|chr1:320000-330000 bin139317|ce10|chr1:330000-340000 bin139318|ce10|chr1:340000-350000 bin139319|ce10|chr1:350000-360000 bin139320|ce10|chr1:360000-370000 bin139321|ce10|chr1:370000-380000 bin139322|ce10|chr1:380000-390000 bin139323|ce10|chr1:390000-400000 bin139324|ce10|chr1:400000-410000 bin139325|ce10|chr1:410000-420000 bin139326|ce10|chr1:420000-430000 bin139327|ce10|chr1:430000-440000 bin139328|ce10|chr1:440000-450000 bin139329|ce10|chr1:450000-460000 bin139330|ce10|chr1:460000-470000 bin139331|ce10|chr1:470000-480000 bin139332|ce10|chr1:480000-490000 bin139333|ce10|chr1:490000-500000 bin139334|ce10|chr1:500000-510000 bin139335|ce10|chr1:510000-520000 bin139336|ce10|chr1:520000-530000 bin139337|ce10|chr1:530000-540000 bin139338|ce10|chr1:540000-550000 bin139339|ce10|chr1:550000-560000 bin139340|ce10|chr1:560000-570000 bin139341|ce10|chr1:570000-580000 bin139342|ce10|chr1:580000-590000 bin139343|ce10|chr1:590000-600000 bin139344|ce10|chr1:600000-610000 bin139345|ce10|chr1:610000-620000 bin139346|ce10|chr1:620000-630000 bin139347|ce10|chr1:630000-640000 bin139348|ce10|chr1:640000-650000 bin139349|ce10|chr1:650000-660000 bin139350|ce10|chr1:660000-670000 bin139351|ce10|chr1:670000-680000 bin139352|ce10|chr1:680000-690000 bin139353|ce10|chr1:690000-700000 bin139354|ce10|chr1:700000-710000 bin139355|ce10|chr1:710000-720000 bin139356|ce10|chr1:720000-730000 bin139357|ce10|chr1:730000-740000 bin139358|ce10|chr1:740000-750000 bin139359|ce10|chr1:750000-760000 bin139360|ce10|chr1:760000-770000 bin139361|ce10|chr1:770000-780000 bin139362|ce10|chr1:780000-790000 bin139363|ce10|chr1:790000-800000 bin139364|ce10|chr1:800000-810000 bin139365|ce10|chr1:810000-820000 bin139366|ce10|chr1:820000-830000 bin139367|ce10|chr1:830000-840000 bin139368|ce10|chr1:840000-850000 bin139369|ce10|chr1:850000-860000 bin139370|ce10|chr1:860000-870000 bin139371|ce10|chr1:870000-880000 bin139372|ce10|chr1:880000-890000 bin139373|ce10|chr1:890000-900000 bin139374|ce10|chr1:900000-910000 bin139375|ce10|chr1:910000-920000 bin139376|ce10|chr1:920000-930000 bin139377|ce10|chr1:930000-940000 bin139378|ce10|chr1:940000-950000 bin139379|ce10|chr1:950000-960000 bin139380|ce10|chr1:960000-970000 bin139381|ce10|chr1:970000-980000 bin139382|ce10|chr1:980000-990000
。。。。。。。
The OnTAD output has five columns:
startpos endpos TADlevel TADmean TADscore
./OnTAD chr18_KR.matrix -penalty 0.1 -maxsz 200 -o OnTAD_KRnorm_pen0.1_max200_chr18 -bedout 18 78077248 10000
OnTAD
1 13554 0 0.052 230.029
15 85 1 1.267 1.005
15 32 2 1.368 0.357
15 22 3 1.616 0.250
22 32 3 1.487 0.103
32 56 2 1.388 0.066
56 85 2 1.590 0.411
56 79 3 1.384 0.072
79 85 3 1.296 0.089
85 115 1 1.262 1.106
85 97 2 1.492 0.327
97 115 2 1.624 0.420
115 142 1 1.284 0.168
142 181 1 1.204 0.030
181 312 1 1.203 1.557
181 298 2 1.189 1.444
193 211 3 1.235 0.033
199 211 4 1.205 0.009
211 221 3 1.213 0.052
221 227 3 1.492 0.336
241 247 3 1.306 0.335
247 259 3 1.201 0.083
259 265 3 1.205 0.183
265 273 3 1.326 0.240
273 286 3 1.265 0.149
298 312 2 1.328 0.097
312 324 1 1.585 0.844
324 485 1 1.608 1.292
324 469 2 1.391 0.774
324 459 3 1.303 0.523
324 449 4 1.248 0.416
363 373 5 1.235 0.109
373 382 5 1.231 0.145
chia-pe
bedpe2Matrix: Generate the Hi-C style matrix. The output matrix is in triplet sparse format, which is compatible with HiCPlotter.
$ bedpe2Matrix --binsize 10000 --chrsizes chrom_hg19.sizes --ifile in.rmDup.bedpe --oprefix PREFIX --progress
HiCPlotter:Hi-C数据可视化工具https://www.jianshu.com/p/27eb60299cdb
从HiC-Pro的处理结果，我们能够得到不同分辨率下的.bed文件和matrix文件。
其中.bed 文件储存了Hi-C结果各个区域的位置信息：
chr1 20960000 20980000 1049
chr1 20980000 21000000 1050
chr1 21000000 21020000 1051
chr1 21020000 21040000 1052
chr1 21040000 21060000 1053
chr1 21060000 21080000 1054
chr1 21080000 21100000 1055
matrix文件则储存了互作情况，使用HiCPlotter选择.bed文件中的一个区域，即可可视化该区域的互作情况。
1050 1586 1
1050 1589 1
1050 1590 1 (jumps to 1612)
1050 1612 2
其他可以作为输入的数据类型：
正常的Hi-C的matrix文件，HiC-Pro输出的是排列为三列的matrix，正常的Hi-Cmatrix格式也可作为输入。Bedgraph，与Bed文件类似，内容更多Peak File，同样是位置信息，需要进一步注释的话需要输入该格式文件Gene File，位置信息和基因信息，可以输出基因互作的结果
https://zhuanlan.zhihu.com/p/48956574 https://cloud.tencent.com/developer/article/1557268
python2 /HiCPlotter-0.6.2.comparison/HiCPlotter.py -f rawdata_500000.matrix -bed rawdata_500000_abs.bed -n raw -chr chr8 -o raw_chr8 -tri 1 -r 500000 -hmc 1 -mm 10 -ptr 1
https://cloud.tencent.com/developer/article/1455988
#!/bin/bash
export PATH=/home/bioinfor312/miniconda3/bin:$PATH
source activate rna
Rscript /home/bioinfor312/bin/ChIA-PET2_0.9.3/bin/MICC2.R NC*.intra.bedpe NC*.inter.bedpe miccOUT 2 6 1e-10
Rscript /home/bioinfor312/bin/ChIA-PET2_0.9.3/bin/MICC2.R S-1*.intra.bedpe S-1*.inter.bedpe miccOUT 2 6 1e-10
Rscript /home/bioinfor312/bin/ChIA-PET2_0.9.3/bin/MICC2.R S-3*.intra.bedpe S-3*.inter.bedpe miccOUT 2 6 1e-10
Rscript /home/bioinfor312/bin/ChIA-PET2_0.9.3/bin/MICC2.R Z-3*.intra.bedpe Z-3*.inter.bedpe miccOUT 2 6 1e-10