HiNT&hic_breakfinder检测HiC数据中染色体易

参考：

1.HiNT : 只能针对剪切酶：DpnII,MboI,HindIII ；发表于Genome Biology

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data
Github for HiNT

image.png

包括三个子命令：

• HiNT-PRE
• HiNT-CNV
• HiNT-TL

$ hint -h
usage: hint [-h] [--version] {pre,cnv,tl} ...

HiNT --- Hic for copy Number variations and Translocations detection

positional arguments:
  {pre,cnv,tl}  sub-command help
    pre         HiNT for Hi-C data preprocessing: raw Hi-C --> HiC contact matrix and chimeric
                read pairs
    cnv         Copy Number Vairations detection from Hi-C
    tl          Identify translocated chromosomal pairs, and detect the breakpoints in 100kb as
                well as 1bp resolution

optional arguments:
  -h, --help    show this help message and exit
  --version     show program's version number and exit

For command line options of each command, type: hint COMMAND -h

• 输出文件

In the HiNT-TL output directory, you will find

jobname_Translocation_IntegratedBP.txt the final integrated translocation breakpoint
jobname_chrompairs_rankProduct.txt rank product predicted potential translocated chromosome pairs
otherFolders intermediate files used to identify the translocation breakpoints

2.hic_breakfinder : https://github.com/dixonlab/hic_breakfinder ；发表于NG

cmake安装jsoncpp
bamtools安装
Ubuntu:安装Eigen3

主需要三个输入文件：
--bam-file ： 比对结果的bam文件
--exp-file-inter：从box 存储位置下载 https://salkinstitute.app.box.com/s/m8oyv2ypf8o3kcdsybzcmrpg032xnrgx
--exp-file-intra：从box 存储位置下载 https://salkinstitute.app.box.com/s/m8oyv2ypf8o3kcdsybzcmrpg032xnrgx

网速慢，下载花时间

image.png

### 帮助信息：
/public/home/kcao/tools/HiCTranslocations/hic_breakfinder/hic_breakfinder_done/bin/hic_breakfinder

Required options:
--bam-file [input bam file]
--exp-file-inter [Inter-chromosomal 1Mb expectation file]
--exp-file-intra [Intra-chromosomal 100kb expectation file]
--name [output file name prefix, will append with *.super_matrix.txt and *.SR.txt]

HiNT实践

目的： 从bedpe or bam 文件，计算易位现象

Step1:安装HiNT :

参考：https://github.com/parklab/HiNT#dependencies

## R依赖包
mgcv, strucchange, doParallel, Cairo, foreach

## 其他工具
pip install HiNT-Package
conda install -c bioconda pairix

Step2：下载必要的输入文件

Download reference files used in HiNT HERE

• Download HiNT references HERE. Only hg19, hg38 and mm10 are available currently. Unzip it $ unzip hg19.zip
  image.png
• Download HiNT background matrices HERE. Only hg19, hg38 and mm10 are available currently. Unzip it $ unzip hg19.zip

image.png

Step3: 运行

### 帮助信息
$  hint tl -h
usage: hint tl [-h] -m MATRIXFILE --refdir REFERENCEDIR [-e {DpnII,MboI,HindIII}]
               [-f {cooler,juicer}] --ppath PAIRIXPATH [-g {hg38,hg19,mm10}] [--chimeric CHIMERIC]
               --backdir BACKGROUNDINTERCHROMMATRIXDIR [-c CUTOFF] [-o OUTDIR] [-n NAME]
               [-p THREADS]

### 运行
$ nohup hint tl -m /public/home/kcao/Work/Pyroptosis_3D/20200794_Hi-C/03_juicer_format/B1_L7_A001.inter.clean.bedpe.hic -f juicer --refdir ./hg19_ref/ --backdir ./hg19_bg/ -g hg19 -n B1 -c 0.05 --ppath ~/miniconda3/envs/R_env/bin/pairix -p 12 -o HiNTtransl_juicerOUTPUT &

Step4: 结果文件

结果输出11个易位发生位点

image.png
image.png

hic_breakfinder 实践

目的：从bedpe 文件中检测易位位点

• Step1： 准备输入文件

## step1.1 : 转换bam格式（bedtools bedpeToBam : bedpe转换成bam）
$ echo "bedpeToBam -i  /public/home/kcao/Work/Pyroptosis_3D/20200794_Hi-C/02_dlo_hic_result/B1_L7_A001_result/03.NoiseReduce/B1_L7_A001.clean.bedpe -g /public/home/kcao/Work/Pyroptosis_3D/20200794_Hi-C/02_dlo_hic_result/B1_L7_A001_result/0a.EnzymeFragment/B1_L7_A001.TTAA.ChrSize.bed > B1_L7_A001.bam"| qsub -d . -N bedpetobam

• Step2：下载Inter-chromosomal 1Mb expectation file，Intra-chromosomal 100kb expectation file

## Tips:网速比较慢
https://salkinstitute.app.box.com/s/m8oyv2ypf8o3kcdsybzcmrpg032xnrgx

• Step3：运行程序

##### Step2:运行程序
$ echo "/public/home/kcao/tools/HiCTranslocations/hic_breakfinder/hic_breakfinder_done/bin/hic_breakfinder --bam-file B1_L7_A001.bam --exp-file-inter inter_expect_1Mb.hg19.txt --exp-file-intra intra_expect_100kb.hg19.txt --name hic_breakfinder_B1_output" | qsub -d . -N hic_breakfinder

• Step4： 结果

Here we will describe the meaning of column of the line:
1 - Log-odds score of the rearrangement call. This is can be thought of as the "strength" of the call.
2 - column chromosome
3 - column start
4 - column end
5 - column strand
6 - row chromosome
7 - row start
8 - row end
9 - row strand
10 - resolution of the call (minimal bin size for which this call is made).

image.png

思考：

• 不同工具，结果检测易位数目不同， hic_breakfinder,HiNT 比HiCTrans 效果更好一些
• 软件安装比较麻烦，特别是hic_breakfinder, 编译一直报错.

欢迎评论交流~😀