20191230对AS类型进行定义

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20191230对AS类型进行定义

前面通过Blast的方法对可变剪切在不同亚基因组间的保守性进行了分类，然后对每一类基因定义了一个概念，这个概念是紧紧围绕多倍化过程中，可变剪切在二倍中同源基因和四倍体同源基因的变化情况

第一类比较保守的AS

conservation AS pattern

筛选条件

匹配长度大于200bp
相似度大于90%
覆盖度超过85%

代码

## 在所有基因组中都保守的IR对应的bed
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]>=1&&a[i][2]>=1&&a[i][1]>=1)print i}}' >converse/1_1
## 都不发生IR事件的基因
cat 1_1.bed  2_2.bed  4_2.bed 1_3.bed  2_3.bed  5_1.bed 1_4.bed  3_2.bed  5_2.bed 2_1.bed  4_1.bed A2.bed At.bed D5.bed Dt.bed|awk '{print $NF}'|grep "Ghir_D" |awk -F "_" '$1~/Ghir/{print $1"_"$2}'|sort |uniq |xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >tmp_Dt
cat 1_1.bed  2_2.bed  4_2.bed 1_3.bed  2_3.bed  5_1.bed 1_4.bed  3_2.bed  5_2.bed 2_1.bed  4_1.bed A2.bed At.bed D5.bed Dt.bed|awk '{print $NF}'|grep "Ghir_A" |awk -F "_" '$1~/Ghir/{print $1"_"$2}'|sort |uniq |xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >tmp_At
cat 1_1.bed  2_2.bed  4_2.bed 1_3.bed  2_3.bed  5_1.bed 1_4.bed  3_2.bed  5_2.bed 2_1.bed  4_1.bed A2.bed At.bed D5.bed Dt.bed|awk '{print $NF}'|grep "Gor" |awk -F "_" '{print $1}'|sort |uniq |xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >tmp_D5
cat 1_1.bed  2_2.bed  4_2.bed 1_3.bed  2_3.bed  5_1.bed 1_4.bed  3_2.bed  5_2.bed 2_1.bed  4_1.bed A2.bed At.bed D5.bed Dt.bed|awk '{print $NF}'|grep "evm" |awk -F "_" '{print $1}'|sort |uniq |xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >tmp_A2
cat tmp* |sort |uniq |cat - ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold |sort |uniq -u >../converseBed/1_2
## 只在A2与At中发生
awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $0}' A2_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]==0&&a[i][0]>=1&&a[i][2]==0)print i}}' >converse/1_3
## 只在D5与Dt中发生
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]==0&&a[i][1]>=1)print i}}' >converse/1_4

做成bed文件

## 在所有基因组中都保守的IR对应的bed
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]>=1&&a[i][2]>=1&&a[i][1]>=1)print i}}' |xargs  -I {} grep {} Dt_query_blast.txt| awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/1_1.bed

## 只在A2与At中发生
awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $0}' A2_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]==0&&a[i][0]>=1&&a[i][2]==0)print i}}'|xargs  -I {} grep {} A2_query_blast.txt |awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/1_3.bed

## 只在D5与Dt中发生
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]==0&&a[i][1]>=1)print i}}' |xargs  -I {} grep {} Dt_query_blast.txt| awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/1_4.bed

第二类多倍化后四倍体中AS发生丢失

AS loose

symmetry loose
At asymmetry loose
Dt asymmetry loose

代码

## Dt中AS 丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]==0&&a[i][0]>=1&&a[i][1]>=1)print i}}' >converse/2_1
## At中AS 丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]>=1&&a[i][1]>=1)print i}}'  >converse/2_2
## At与Dt都丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $0}' A2_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][1]>=1&&a[i][2]==0)print i}}' >converse/2_3

做成bed文件

## Dt中AS 丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]==0&&a[i][0]>=1&&a[i][1]>=1)print i}}' |xargs  -I {} grep {} At_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/2_1.bed

## At中AS 丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]>=1&&a[i][1]>=1)print i}}'  |xargs  -I {} grep {} Dt_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/2_2.bed

## At与Dt都丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $0}' A2_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][1]>=1&&a[i][2]==0)print i}}'|xargs  -I {} grep {} A2_query_blast.txt | awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq   >converseBed/2_3.bed

第三类多倍化后四倍体AS重新获得

AS gain

symmetry gain
At asymmetry gain
Dt asymmetry gain

代码

:warning:单个基因组存在的事件得再converseBed目录下运行

## 只有At 获得新的AS事件
cat 1_1.bed 1_3.bed  2_1.bed 3_2.bed 4_1.bed 4_2.bed 5_2.bed |awk -F "\t" '$5~/Ghir_A/{print ">"$5}'|cat - ../At_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' >../converse/3_1
## At与Dt 获得同样的AS事件
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]==0&&a[i][2]==0&&a[i][0]>=1)print i}}'  >converse/3_2
## 只有Dt 获得新的AS事件
cat 1_1.bed 1_4.bed 2_2.bed 3_2.bed 4_1.bed 4_2.bed 5_1.bed|awk -F "\t" '$5~/Ghir_D/{print ">"$5}' |cat - ../Dt_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' >../converse/3_3

做成bed文件

## At与Dt 获得同样的AS事件
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]==0&&a[i][2]==0&&a[i][0]>=1)print i}}'|xargs  -I {} grep {} Dt_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq   >converseBed/3_2.bed

第四类四倍体中两个亚基因组有趋同效应

convergence effect

convergence to gain
convergence to loose

代码

## D5中不存在
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]>=1&&a[i][0]>=1&&a[i][1]==0)print i}}' >converse/4_1
## A2中不存在
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]>=1&&a[i][2]==0&&a[i][0]>=1)print i}}' >converse/4_2
## 只有A2中有
cat 1_1.bed 1_3.bed 2_1.bed 2_2.bed 2_3.bed 4_1.bed 5_1.bed|awk -F "\t" '$5~/evm/{print ">"$5}'|cat - ../A2_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g'  >../converse/4_3
## 只有D5中有
cat 1_1.bed 1_4.bed 2_1.bed 2_2.bed 2_3.bed 4_2.bed 5_2.bed|awk -F "\t" '$5~/Gor/{print ">"$5}'|cat - ../D5_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' >../converse/4_4

做成bed文件

## D5中不存在
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]>=1&&a[i][0]>=1&&a[i][1]==0)print i}}' |xargs  -I {} grep {} At_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq >converseBed/4_1.bed

## A2中不存在
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]>=1&&a[i][2]==0&&a[i][0]>=1)print i}}'|xargs  -I {} grep {} Dt_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq   >converseBed/4_2.bed

第五类

AS事件在不同亚基因组间保守

## 只在A2与Dt中保守
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]>=1&&a[i][1]==0)print i}}' >converse/5_1
## 只在D5与At中保守
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]==0&&a[i][1]>=1&&a[i][0]==0)print i}}' >converse/5_2

做成bed文件

## 只在A2与Dt中保守
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]>=1&&a[i][1]==0)print i}}'|xargs  -I {} grep {} Dt_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/5_1.bed
## 只在D5与At中保守
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]==0&&a[i][1]>=1&&a[i][0]==0)print i}}'|xargs  -I {} grep {} At_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/5_2.bed

求只在单个基因组中的剪切事件

在只某一个基因组中保守的类型，先统计与其他基因组中保守的类型的bed1文件，然后剔除掉这些就是只在某个基因组中单独存在的剪切事件了。

## At和其他基因组中共有的类型
1_1 1_3 2_1 3_2 4_1 4_2 5_2 
cat 1_1.bed 1_3.bed  2_1.bed 3_2.bed 4_1.bed 4_2.bed 5_2.bed |awk -F "\t" '$5~/Ghir_A/{print ">"$5}'|cat - ../At_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' |awk -F "_" '{print $3"_"$4,$5,$6,$8,$0}' OFS="\t" >At.bed 
## Dt和其他基因组中共有的类型
cat 1_1.bed 1_4.bed 2_2.bed 3_2.bed 4_1.bed 4_2.bed 5_1.bed|awk -F "\t" '$5~/Ghir_D/{print ">"$5}' |cat - ../Dt_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' |awk -F "_" '{print $3"_"$4,$5,$6,$8,$0}' OFS="\t" >Dt.bed
## A2和其他基因组中共有的类型
cat 1_1.bed 1_3.bed 2_1.bed 2_2.bed 2_3.bed 4_1.bed 5_1.bed|awk -F "\t" '$5~/evm/{print ">"$5}'|cat - ../A2_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' |awk -F "_" '{print $2,$3,$4,$6,$0}' OFS="\t" >A2.bed
## D5和其他基因组共有的类型
cat 1_1.bed 1_4.bed 2_1.bed 2_2.bed 2_3.bed 4_2.bed 5_2.bed|awk -F "\t" '$5~/Gor/{print ">"$5}'|cat - ../D5_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' |awk -F "_" '{print $2,$3,$4,$6,$0}' OFS="\t" >D5.bed

A2与At 、D5与Dt间保守的剪切事件

## A2与At中都存在的保守事件
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]>=1)print i}}' >converse/A2_At_converse.txt
## D5与Dt中都存在的保守事件
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]>=1)print i}}' >converse/D5_Dt_converse.txt

统计基因数与事件数

总共有16类，对每一类都统计一下对应的事件的数目

##第一大类
wc -l 1_1 
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 1_1 |sort |uniq |wc -l
wc -l 1_2
wc -l 1_3 
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 1_3 |sort |uniq |wc -l
wc -l 1_4 
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 1_4 |sort |uniq |wc -l
##第二大类
wc -l 2_1
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 2_1 |sort |uniq |wc -l
wc -l 2_2
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 2_2 |sort |uniq |wc -l
wc -l 2_3
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 2_3|sort |uniq |wc -l
##第三大类
wc -l ../converseBed/At.bed
cut -f5 ../converseBed/At.bed|awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}'  |sort |uniq |wc -l
wc -l 3_2
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 3_2 |sort |uniq |wc -l
wc -l ../converseBed/Dt.bed
cut -f5  ../converseBed/Dt.bed |awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}'|sort |uniq |wc -l
## 第四大类
wc -l 4_1
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 4_1 |sort |uniq |wc -l
wc -l 4_2
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 4_2 |sort |uniq |wc -l
wc -l ../converseBed/A2.bed
cut -f5 ../converseBed/A2.bed |awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' |sort |uniq |wc -l
wc -l ../converseBed/D5.bed
cut -f5 ../converseBed/D5.bed |awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' |sort |uniq |wc -l

intronR

事件

基因数目

事件数目

1_1

840

1489

1_2

8071

1_3

1122

1869

1_4

1438

2247

2_1

651

977

2_2

600

861

2_3

1043

1541

3858

7683

3_2

1038

1571

3924

8053

4_1

579

876

4_2

825

1245

4087

8451

5066

10217

ExonS

事件

基因数目

事件数目

1_1

1_2

15390

1_3

103

108

1_4

235

254

2_1

2_2

2_3

712

800

3_2

661

740

4_1

4_2

656

759

1406

1648

AltA

事件

基因数目

事件数目

1_1

137

167

1_2

12517

1_3

212

262

1_4

423

477

2_1

110

2_2

2_3

172

198

1805

2312

3_2

367

421

1777

2359

4_1

4_2

218

261

1555

2126

2127

2809

AltD

事件

基因数目

事件数目

1_1

1_2

13275

1_3

169

216

1_4

284

331

2_1

2_2

2_3

125

146

1671

2122

3_2

316

364

1714

2243

4_1

4_2

148

181

1291

1688

1550

1934

对同源基因间的剪切取交集

Dt中的可变剪切

1_1 1_4 2_2 3_2 3_3 4_1 4_2 5_1

At中的可变剪切

1_1 1_3 2_1 3_1 3_2 4_1 4_2 5_2

D5中的可变剪切

1_1 1_4 2_1 2_2 2_3 4_2 4_4 5_2

A2中的可变剪切

1_1 1_3 2_1 2_2 2_3 4_1 4_3 5_1

Previous第三个结果 NextAS保守程度的统计

Last updated 5 years ago

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第一类比较保守的AS

conservation AS pattern

筛选条件

匹配长度大于200bp
相似度大于90%
覆盖度超过85%

代码

## 在所有基因组中都保守的IR对应的bed
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]>=1&&a[i][2]>=1&&a[i][1]>=1)print i}}' >converse/1_1
## 都不发生IR事件的基因
cat 1_1.bed  2_2.bed  4_2.bed 1_3.bed  2_3.bed  5_1.bed 1_4.bed  3_2.bed  5_2.bed 2_1.bed  4_1.bed A2.bed At.bed D5.bed Dt.bed|awk '{print $NF}'|grep "Ghir_D" |awk -F "_" '$1~/Ghir/{print $1"_"$2}'|sort |uniq |xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >tmp_Dt
cat 1_1.bed  2_2.bed  4_2.bed 1_3.bed  2_3.bed  5_1.bed 1_4.bed  3_2.bed  5_2.bed 2_1.bed  4_1.bed A2.bed At.bed D5.bed Dt.bed|awk '{print $NF}'|grep "Ghir_A" |awk -F "_" '$1~/Ghir/{print $1"_"$2}'|sort |uniq |xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >tmp_At
cat 1_1.bed  2_2.bed  4_2.bed 1_3.bed  2_3.bed  5_1.bed 1_4.bed  3_2.bed  5_2.bed 2_1.bed  4_1.bed A2.bed At.bed D5.bed Dt.bed|awk '{print $NF}'|grep "Gor" |awk -F "_" '{print $1}'|sort |uniq |xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >tmp_D5
cat 1_1.bed  2_2.bed  4_2.bed 1_3.bed  2_3.bed  5_1.bed 1_4.bed  3_2.bed  5_2.bed 2_1.bed  4_1.bed A2.bed At.bed D5.bed Dt.bed|awk '{print $NF}'|grep "evm" |awk -F "_" '{print $1}'|sort |uniq |xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >tmp_A2
cat tmp* |sort |uniq |cat - ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold |sort |uniq -u >../converseBed/1_2
## 只在A2与At中发生
awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $0}' A2_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]==0&&a[i][0]>=1&&a[i][2]==0)print i}}' >converse/1_3
## 只在D5与Dt中发生
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]==0&&a[i][1]>=1)print i}}' >converse/1_4

做成bed文件

## 在所有基因组中都保守的IR对应的bed
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]>=1&&a[i][2]>=1&&a[i][1]>=1)print i}}' |xargs  -I {} grep {} Dt_query_blast.txt| awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/1_1.bed

## 只在A2与At中发生
awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $0}' A2_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]==0&&a[i][0]>=1&&a[i][2]==0)print i}}'|xargs  -I {} grep {} A2_query_blast.txt |awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/1_3.bed

## 只在D5与Dt中发生
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]==0&&a[i][1]>=1)print i}}' |xargs  -I {} grep {} Dt_query_blast.txt| awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/1_4.bed

第二类多倍化后四倍体中AS发生丢失

AS loose

symmetry loose
At asymmetry loose
Dt asymmetry loose

代码

## Dt中AS 丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]==0&&a[i][0]>=1&&a[i][1]>=1)print i}}' >converse/2_1
## At中AS 丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]>=1&&a[i][1]>=1)print i}}'  >converse/2_2
## At与Dt都丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $0}' A2_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][1]>=1&&a[i][2]==0)print i}}' >converse/2_3

做成bed文件

## Dt中AS 丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]==0&&a[i][0]>=1&&a[i][1]>=1)print i}}' |xargs  -I {} grep {} At_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/2_1.bed

## At中AS 丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]>=1&&a[i][1]>=1)print i}}'  |xargs  -I {} grep {} Dt_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/2_2.bed

## At与Dt都丢失
awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $0}' A2_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][1]>=1&&a[i][2]==0)print i}}'|xargs  -I {} grep {} A2_query_blast.txt | awk '$7>200&&$8>90&&$9>85&&$2!~/evm.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq   >converseBed/2_3.bed

第三类多倍化后四倍体AS重新获得

AS gain

symmetry gain
At asymmetry gain
Dt asymmetry gain

代码

:warning:单个基因组存在的事件得再converseBed目录下运行

## 只有At 获得新的AS事件
cat 1_1.bed 1_3.bed  2_1.bed 3_2.bed 4_1.bed 4_2.bed 5_2.bed |awk -F "\t" '$5~/Ghir_A/{print ">"$5}'|cat - ../At_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' >../converse/3_1
## At与Dt 获得同样的AS事件
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]==0&&a[i][2]==0&&a[i][0]>=1)print i}}'  >converse/3_2
## 只有Dt 获得新的AS事件
cat 1_1.bed 1_4.bed 2_2.bed 3_2.bed 4_1.bed 4_2.bed 5_1.bed|awk -F "\t" '$5~/Ghir_D/{print ">"$5}' |cat - ../Dt_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' >../converse/3_3

做成bed文件

## At与Dt 获得同样的AS事件
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]==0&&a[i][2]==0&&a[i][0]>=1)print i}}'|xargs  -I {} grep {} Dt_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq   >converseBed/3_2.bed

第四类四倍体中两个亚基因组有趋同效应

convergence effect

convergence to gain
convergence to loose

代码

## D5中不存在
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]>=1&&a[i][0]>=1&&a[i][1]==0)print i}}' >converse/4_1
## A2中不存在
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]>=1&&a[i][2]==0&&a[i][0]>=1)print i}}' >converse/4_2
## 只有A2中有
cat 1_1.bed 1_3.bed 2_1.bed 2_2.bed 2_3.bed 4_1.bed 5_1.bed|awk -F "\t" '$5~/evm/{print ">"$5}'|cat - ../A2_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g'  >../converse/4_3
## 只有D5中有
cat 1_1.bed 1_4.bed 2_1.bed 2_2.bed 2_3.bed 4_2.bed 5_2.bed|awk -F "\t" '$5~/Gor/{print ">"$5}'|cat - ../D5_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' >../converse/4_4

做成bed文件

## D5中不存在
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]>=1&&a[i][0]>=1&&a[i][1]==0)print i}}' |xargs  -I {} grep {} At_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq >converseBed/4_1.bed

## A2中不存在
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]>=1&&a[i][2]==0&&a[i][0]>=1)print i}}'|xargs  -I {} grep {} Dt_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq   >converseBed/4_2.bed

第五类

AS事件在不同亚基因组间保守

## 只在A2与Dt中保守
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]>=1&&a[i][1]==0)print i}}' >converse/5_1
## 只在D5与At中保守
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]==0&&a[i][1]>=1&&a[i][0]==0)print i}}' >converse/5_2

做成bed文件

## 只在A2与Dt中保守
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]==0&&a[i][2]>=1&&a[i][1]==0)print i}}'|xargs  -I {} grep {} Dt_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/5_1.bed
## 只在D5与At中保守
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][2]==0&&a[i][1]>=1&&a[i][0]==0)print i}}'|xargs  -I {} grep {} At_query_blast.txt|awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $1"\n"$2}'|awk -F "_" '$1~/Ghir/{print $3"_"$4,$5,$6,$8,$0}$1!~/Ghir/{print $2,$3,$4,$6,$0}' OFS="\t" |sort |uniq  >converseBed/5_2.bed

求只在单个基因组中的剪切事件

在只某一个基因组中保守的类型，先统计与其他基因组中保守的类型的bed1文件，然后剔除掉这些就是只在某个基因组中单独存在的剪切事件了。

## At和其他基因组中共有的类型
1_1 1_3 2_1 3_2 4_1 4_2 5_2 
cat 1_1.bed 1_3.bed  2_1.bed 3_2.bed 4_1.bed 4_2.bed 5_2.bed |awk -F "\t" '$5~/Ghir_A/{print ">"$5}'|cat - ../At_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' |awk -F "_" '{print $3"_"$4,$5,$6,$8,$0}' OFS="\t" >At.bed 
## Dt和其他基因组中共有的类型
cat 1_1.bed 1_4.bed 2_2.bed 3_2.bed 4_1.bed 4_2.bed 5_1.bed|awk -F "\t" '$5~/Ghir_D/{print ">"$5}' |cat - ../Dt_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' |awk -F "_" '{print $3"_"$4,$5,$6,$8,$0}' OFS="\t" >Dt.bed
## A2和其他基因组中共有的类型
cat 1_1.bed 1_3.bed 2_1.bed 2_2.bed 2_3.bed 4_1.bed 5_1.bed|awk -F "\t" '$5~/evm/{print ">"$5}'|cat - ../A2_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' |awk -F "_" '{print $2,$3,$4,$6,$0}' OFS="\t" >A2.bed
## D5和其他基因组共有的类型
cat 1_1.bed 1_4.bed 2_1.bed 2_2.bed 2_3.bed 4_2.bed 5_2.bed|awk -F "\t" '$5~/Gor/{print ">"$5}'|cat - ../D5_intron_junction.fasta|grep ">"|sort|uniq -u|sed 's/>//g' |awk -F "_" '{print $2,$3,$4,$6,$0}' OFS="\t" >D5.bed

A2与At 、D5与Dt间保守的剪切事件

## A2与At中都存在的保守事件
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_A.*/{print $0}' At_query_blast.txt |awk '$2~/evm/{a[$1][0]+=1}$2~/Ghir_D/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][0]>=1)print i}}' >converse/A2_At_converse.txt
## D5与Dt中都存在的保守事件
awk '$7>200&&$8>90&&$9>85&&$2!~/Ghir_D.*/{print $0}' Dt_query_blast.txt |awk '$2~/Ghir_A/{a[$1][0]+=1}$2~/evm/{a[$1][2]+=1}$2~/Gor/{a[$1][1]+=1}END{for(i in a){if(a[i][1]>=1)print i}}' >converse/D5_Dt_converse.txt

统计基因数与事件数

总共有16类，对每一类都统计一下对应的事件的数目

##第一大类
wc -l 1_1 
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 1_1 |sort |uniq |wc -l
wc -l 1_2
wc -l 1_3 
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 1_3 |sort |uniq |wc -l
wc -l 1_4 
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 1_4 |sort |uniq |wc -l
##第二大类
wc -l 2_1
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 2_1 |sort |uniq |wc -l
wc -l 2_2
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 2_2 |sort |uniq |wc -l
wc -l 2_3
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 2_3|sort |uniq |wc -l
##第三大类
wc -l ../converseBed/At.bed
cut -f5 ../converseBed/At.bed|awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}'  |sort |uniq |wc -l
wc -l 3_2
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 3_2 |sort |uniq |wc -l
wc -l ../converseBed/Dt.bed
cut -f5  ../converseBed/Dt.bed |awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}'|sort |uniq |wc -l
## 第四大类
wc -l 4_1
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 4_1 |sort |uniq |wc -l
wc -l 4_2
awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' 4_2 |sort |uniq |wc -l
wc -l ../converseBed/A2.bed
cut -f5 ../converseBed/A2.bed |awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' |sort |uniq |wc -l
wc -l ../converseBed/D5.bed
cut -f5 ../converseBed/D5.bed |awk -F "_" '$1~/Ghir/{print $1"_"$2}$1!~/Ghir/{print $1}' |sort |uniq |wc -l

intronR

事件

基因数目

事件数目

1_1

840

1489

1_2

8071

1_3

1122

1869

1_4

1438

2247

2_1

651

977

2_2

600

861

2_3

1043

1541

3858

7683

3_2

1038

1571

3924

8053

4_1

579

876

4_2

825

1245

4087

8451

5066

10217

ExonS

事件

基因数目

事件数目

1_1

1_2

15390

1_3

103

108

1_4

235

254

2_1

2_2

2_3

712

800

3_2

661

740

4_1

4_2

656

759

1406

1648

AltA

事件

基因数目

事件数目

1_1

137

167

1_2

12517

1_3

212

262

1_4

423

477

2_1

110

2_2

2_3

172

198

1805

2312

3_2

367

421

1777

2359

4_1

4_2

218

261

1555

2126

2127

2809

AltD

事件

基因数目

事件数目

1_1

1_2

13275

1_3

169

216

1_4

284

331

2_1

2_2

2_3

125

146

1671

2122

3_2

316

364

1714

2243

4_1

4_2

148

181

1291

1688

1550

1934

对同源基因间的剪切取交集

Dt中的可变剪切

1_1 1_4 2_2 3_2 3_3 4_1 4_2 5_1

At中的可变剪切

1_1 1_3 2_1 3_1 3_2 4_1 4_2 5_2

D5中的可变剪切

1_1 1_4 2_1 2_2 2_3 4_2 4_4 5_2

A2中的可变剪切

1_1 1_3 2_1 2_2 2_3 4_1 4_3 5_1