> 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/ke-bian-jian-qie/shu-ju-chu-li-liu-cheng/fen-xi-tong-yuan-ji-yin-fa-sheng-ir-de-pin-shuai.md).

# 分析同源基因中发生IR事件的频率

首先根据已经鉴定好的IR事件，和对应的亚基因组同源基因；分别去看每个棉种中对应基因发生IR的频率或者是数目

就可以大致的将同源基因进行一个分类

1. 四个基因组中都频繁的发生IR事件 >10
2. 四个基因组的基因都不发生IR事件
3. 只有个别基因组频繁的发生了IR事件
4. At与A2 频繁的发生IR事件
5. Dt与D5 频繁的发生IR事件
6. A2与D5 比较频繁发生
7. At与Dt 频繁的发生
8. 各个基因组发生的频数相差都不大

## 同源基因中IR事件数目的统计

```bash
## 将所有棉种的IR事件合并到一个文件中
awk '$3~/IntronR/{print $2}' ../TM-1/end_third |sort |uniq -c |awk '{print $2"\t"$1}' >intronR_count.txt 
awk '$3~/IntronR/{print $2}' ../D5/end_third |sort |uniq -c |awk '{print $2"\t"$1}' >>intronR_count.txt 
awk '$3~/IntronR/{print $2}' ../A2/end_third  |sort |uniq -c |awk '{print $2"\t"$1}' >>intronR_count.txt
## 之后使用自己写的python脚本跑
python Count_homologe_IRcount.py  intronR_count.txt ../GhDt_Gr_GhAt_Ga_end_noScaffold  1
```

## 比较频数相差不大的这些基因中比较保守的IR事件

### 1.首先都没有发生IR事件的同源基因

```bash
awk '$2==0&&$4==0&&$6==0&&$8==0{print $0}' 1
```

### 2.都发生了IR事件但是

```bash
## 数目上相差不超过log2 阀值
awk '$2!=0&&$4!=0&&$6!=0&&$8!=0{if(($2/$4<2&&$2/$4>0.5)&&($2/$6<2&&$2/$6>0.5)&&($2/$8<2&&$2/$8>0.5)&&($4/$6<2&&$4/$6>0.5)&&($4/$6<2&&$4/$8>0.5)&&($6/$8<2&&$6/$8>0.5)){print $0}}' 1
## 存在两倍差异
awk '$2!=0&&$4!=0&&$6!=0&&$8!=0{if(($2/$4<2&&$2/$4>0.5)&&($2/$6<2&&$2/$6>0.5)&&($2/$8<2&&$2/$8>0.5)&&($4/$6<2&&$4/$6>0.5)&&($4/$6<2&&$4/$8>0.5)&&($6/$8<2&&$6/$8>0.5)){}else{print $0}}' 1
```

### 3. 单个基因组有IR而其他3个基因组全为0

```bash
## Dt
awk '$2!=0&&$4==0&&$6==0&&$8==0{print $0}' 1 
## D5
awk '$2==0&&$4!=0&&$6==0&&$8==0{print $0}' 1 
## At
awk '$2==0&&$4==0&&$6!=0&&$8==0{print $0}' 1
## A2
awk '$2==0&&$4==0&&$6==0&&$8!=0{print $0}' 1
```

### 4 两个基因组为0，而另外两个不为0

```bash
## A2=At=0
awk '$2!=0&&$4!=0&&$6==0&&$8==0{print $0}' 1
## A2=D5=0
awk '$2!=0&&$4==0&&$6!=0&&$8==0{print $0}' 1
## A2=Dt=0
awk '$2==0&&$4!=0&&$6!=0&&$8==0{print $0}' 1
## D5=Dt=0
awk '$2==0&&$4==0&&$6!=0&&$8!=0{print $0}' 1
## D5=At=0
awk '$2!=0&&$4==0&&$6==0&&$8!=0{print $0}' 1
## Dt=At=0
```

### 5.只有一个基因组为0，其他不为0

```bash
## Dt=0
awk '$2==0&&$4!=0&&$6!=0&&$8!=0{print $0}' 1
## D5=0
awk '$2!=0&&$4==0&&$6!=0&&$8!=0{print $0}' 1
## At=0
awk '$2!=0&&$4!=0&&$6==0&&$8!=0{print $0}' 1
## A2=0
awk '$2!=0&&$4!=0&&$6!=0&&$8==0{print $0}' 1
```

## 还是得把0换成一个小一点的数去算

把所有的0都换成0.5，然后算

### 1.都没有发生IR的基因对

```bash
awk '$2==0.5&&$4==0.5&&$6==0.5&&$8==0.5{print $0}' 1 >class1
```

### 2.统计各个基因组中频繁发生IR的基因对

```bash
## 排除那些都没有发生IR的基因后，亚基因组IR数目没有明显差异
##awk '$2!=0.5&&$4!=0.5&&$6!=0.5&&$8!=0.5{if(($2/$4<2&&$2/$4>0.5)&&($2/$6<2&&$2/$6>0.5)&&($2/$8<2&&$2/$8>0.5)&&($4/$6<2&&$4/$6>0.5)&&($4/$6<2&&$4/$8>0.5)&&($6/$8<2&&$6/$8>0.5)){print $0}}' 1
## 只在Dt中频繁发生IR的基因对
awk '{if(($2/$4>2)&&($2/$6>2)&&($2/$8>2)){print $0}}' 1 >class2
## 只在D5中频繁发生IR的
awk '{if(($4/$2>2)&&($4/$6>2)&&($4/$8>2)){print $0}}' 1 >class3
## 只在At中频繁发生IR的
awk '{if(($6/$2>2)&&($6/$4>2)&&($6/$8>2)){print $0}}' 1 >class4 
## 只在A2中频繁发生IR
awk '{if(($8/$2>2)&&($8/$4>2)&&($8/$6>2)){print $0}}' 1 >class5
## 在祖先基因组 A2 D5中频繁发生IR 而At与Dt很少
awk '{if(($8/$6>2)&&($4/$2>2)){print $0}}' 1 >class6
## 在祖先中发生的少，而后代频繁的
awk '{if(($8/$6<0.5)&&($4/$2<0.5)){print $0}}' 1 >class7

## 祖先A2 与D5存在差异 而后代不存在
awk '{if(($8/$4<0.5||$8/$4>2)&&($6/$2>0.5&&$6/$2<2)){print $0}}' 1 >class8
## 祖先存在差异，而后代同样存在差异
awk '{if(($8/$4<0.5||$8/$4>2)&&($6/$2<0.5||$6/$2>2)){print $0}}' 1 >class9
## 祖先不存在差异，而后代存在差异
awk '{if(($8/$4>0.5&&$8/$4<2)&&($6/$2<0.5||$6/$2>2)){print $0}}' 1 >class10
## 祖先不存在差异，后代也不存在差异
awk '$2!=0.5&&$4!=0.5&&$6!=0.5&&$8!=0.5{if(($8/$4>0.5&&$8/$4<2)&&($6/$2>0.5&&$6/$2<2)){print $0}}' 1 >class11
```


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