> For the complete documentation index, see [llms.txt](https://zpliu.gitbook.io/booknote/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://zpliu.gitbook.io/booknote/hi-c/ruan-jian/juicer-tools-pre.md).

# pre程序

使用pre程序将HiC-Pro的结果转化成`.hic`文件。

首先需要将HiC-Pro得到的`rawdata`结果转化成pre输入文件格式，同时考虑到hic数据太大，因此写个多进程的python脚本转化一下HiC-Pro的结果

## pre输入文件格式

如果没有酶切的信息的话，就随便使用一个数字对其进行填充

```
<str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2>
```

* str = strand (0 for forward, anything else for reverse)
* chr = chromosome (must be a chromosome in the genome)
* pos = position
* frag = restriction site fragment

## python脚本

大概能够处理最大20G的文件，大了的话还是需要用`split`分割一下；之后再改进这个脚本

* `-s`脚手架前称
* `-i`输入文件
* `-t`进程数
* `-o`输出文件

```bash
python ~/github/zpliuCode/Hi-c/HiCProTojuicer.py -i ./rawdata.allValidPairs -s Scaffold -t 20 -o ~/github/juicer/LSF/test/Gb_HiC-Pro.txt 
## 提交任务
bsub -q high -M 200G -R span[hosts=1] -J Hic-Pro  -n 20 -e %J.err -o %J.out  "python ~/github/zpliuCode/Hi-c/HiCProTojuicer.py -i /data/cotton/MaojunWang/WMJ_fiber3Dgenome/Gb379_0D_HiC_merged_results/hic_results/data/rawdata/rawdata.allValidPairs -s Scaffold -t 20 -o ~/github/juicer/LSF/test/Gb_HiC-Pro.txt"
```

48G的文件还是大了，分4份跑一下看看

```bash
## 查看文件行数
wc -l 文件
## 分割文件
split -行数 文件名
## 批量提交脚本
```

## Pre转化格式

* `-r`指定以10K分辨率进行计算

```bash
java -jar scripts/juicer_tools.jar pre -r 10000 data/Gb_HiC-Pro.txt  data/Gb.hic  Gb_HAU_v2.0_Chrosome.txt
```

### 报错

```bash
........Error: the chromosome combination 1_1 appears in multiple blocks
```

染色体需要排好序，使得程序尽量减少内存的消耗

<http://aidenlab.org/forum.html?place=msg%2F3d-genomics%2FbPAm69WEXVg%2F9_o_RcdrBAAJ>

![NjuOmj.png](https://s1.ax1x.com/2020/07/03/NjuOmj.png)

## 测试数据

```bash
#0D~25D的数据和叶片的数据
/data/cotton/MaojunWang/WMJ_fiber3Dgenome/Gb379_0D_HiC_merged_results/hic_results/data/rawdata
/data/cotton/MaojunWang/WMJ_fiber3Dgenome/Gb379_5D_HiC_merged_results/hic_results/data/rawdata
/data/cotton/MaojunWang/WMJ_fiber3Dgenome/Gb379_10D_HiC_merged_results/hic_results/data/rawdata
/data/cotton/MaojunWang/WMJ_fiber3Dgenome/Gb379_20D_HiC_merged_results/hic_results/data/rawdata
## 叶片数据
/data/cotton/MaojunWang/WMJ_fiber3Dgenome/Gb379_leaf_HiC_merged_results/hic_results/data/rawdata
```

## pre提交LSF任务

```bash
bsub -q high -J pre -e %J.err -o %J.out -n 10 -R span[hosts=1] "java -jar ~/github/juicer/LSF/scripts/juicer_tools.jar  pre -r 10000 --threads 10 ./Gb379_5D_HiC_raw.txt  ./Gb379_5D_HiC_raw.hic ~/github/juicer/LSF/Gb_HAU_v2.0_Chrosome.txt "
```

## HiCCUPs任务

```bash
for i in `ls ./|grep hic`
do
b=`echo $i|sed 's/raw\.hic//g'`loop
bsub -q gpu -J pre -e %J.err -o %J.out -n 5 -R span[hosts=1] "java -jar ~/github/juicer/LSF/scripts/juicer_tools.jar  hiccups -m 500 -r 10000 -f 0.1 -p 2  -i 5 -d 20000   -k KR --threads 5 ./${i}  ./${b}"
done
##使用默认参数跑一下
bsub -q gpu -J pre -e %J.err -o %J.out -n 5 -R span[hosts=1] "java -jar ~/github/juicer/LSF/scripts/juicer_tools.jar  hiccups -m 500 -r 5000,10000 -d 20000,21000 -k KR  -f .1,.1  -p 4,2  -i 7,5  -t 0.02,1.5,1.75,2  --threads 5  -c Gbar_A01,Gbar_A02,Gbar_A03,Gbar_A04,Gbar_A05,Gbar_A06,Gbar_A07,Gbar_A08,Gbar_A09,Gbar_A10,Gbar_A11,Gbar_A12,Gbar_A13,Gbar_D01,Gbar_D02,Gbar_D03,Gbar_D04,Gbar_D05,Gbar_D06,Gbar_D07,Gbar_D08,Gbar_D09,Gbar_D10,Gbar_D11,Gbar_D12,Gbar_D13  ./${i}  ./${b}"
bsub -q gpu -J pre -e %J.err -o %J.out -n 10 -R span[hosts=1] "java -jar ~/github/juicer/LSF/scripts/juicer_tools.jar  hiccups -m 500 -r 10000,25000 --threads 10 ./${i}  ./${b}"
```