生物信息学与算法多组学知识基础NGS

Intervene: BED文件的intersect和绘制韦恩图

2020-03-28  本文已影响0人  浩渺予怀

一、背景介绍

通常,BED文件的overlap/intersect的操作,可以BEDtools intersect功能完成overlap和统计:
Bedtolols intersect: Find overlapping intervals in various ways
2-3个文件H还比较简单,多个BED文件操作起来稍显繁琐。这里介绍一款基于BEDtools功能的软件:Intervene。

Intervene是一个用于intersect多个基因组区域(BED)和基因集的的工具,简而言之,实现韦恩图的功能,这对于我们去寻找交集非常方便,比对寻找多个BED/GTF/GFF/SNP文件(如peaks、SV等)的交并集结果。

软件官方介绍

https://intervene.readthedocs.io/en/latest/introduction.html

功能介绍

主要有3个功能,

(1) venn to compute Venn diagrams of up-to 6 sets

图片.png

(2) upset to compute UpSet plots of multiple sets

图片.png

(3) pairwise to compute and visualize intersections of genomic sets as clustered heatmap

图片.png

三、软件安装

# pip
pip install intervene

# 源码
git clone https://github.com/asntech/intervene.git
cd intervene
python setup.py sdist install
​# 必需的依赖包
Python (=> 2.7 ): https://www.python.org/
BEDTools (Latest version): https://github.com/arq5x/bedtools2
pybedtools (>= 0.7.9): https://daler.github.io/pybedtools/
Pandas (>= 0.16.0): http://pandas.pydata.org/
Seaborn (>= 0.7.1): http://seaborn.pydata.org/
R (>= 3.0): https://www.r-project.org/
R packages including UpSetR, corrplot

四、如何使用

测试数据

H3K27ac.bed
H3K27me3.bed
H3K4me1.bed
H3K4me2.bed
H3K4me3.bed

数据格式
BED数据的格式示例如下

chr1    713131  713668  .       560     .       12.759191       15.7    -1
chr1    713872  714208  .       850     .       23.636091       15.7    -1
chr1    714437  714760  .       850     .       23.623177       100.0   -1
chr1    761967  763114  .       701     .       18.056475       15.7    -1
chr1    820974  826939  .       275     .       2.062345        2.3     -1

intervenn子功能

intervene <subcommand> [options]

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets.
For more details check documentation: http://intervene.readthedocs.io

positional arguments:
  {venn,upset,pairwise}
                        List of subcommands
    venn                Venn diagram of intersection of genomic regions or list sets (upto 6-way).
    upset               UpSet diagram of intersection of genomic regions or list sets.
    pairwise            Pairwise intersection and heatmap of N genomic region sets in <BED/GTF/GFF> format.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -c, --cite            show citation information and exit

一、venn功能:

intervene venn -i example_data/ENCODE_hESC/*bed --output test/venn --save-overlaps

Generating a 5-way "venn" diagram. Please wait...

Done! Please check your results @ test/venn.
Thank you for using Intervene!

# 最多可实现6-way venn
# 基于bedtools功能,可以支持调整bedtools相关的参数,比如-f 

测试图形:

venn

二、upset功能:

intervene upset -i example_data/ENCODE_hESC/*bed --output test/upset

可以把计算的数据导入网站在线绘制

三、pairwise功能

intervene pairwise -i example_data/ENCODE_hESC/*bed --type genomic --compute jaccard --htype tribar --output test/pairwise

测试结果:

pairwise.png

图形三角的朝向可以使用--triangle控制,比如upper;只有设置计算方法为jaccardfisher后才建议使用tribar参数

另外,上述分析结果均会做图的数据,该数据也可以导入在线的网(https://asntech.shinyapps.io/intervene/)进行展示,不过网站有点慢。

参考文献:

Khan A, Mathelier A. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics. 2017;18:287. doi: 10.1186/s12859-017-1708-7

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