To address this gap, we have developed the Intervene tool, which provides an easy and automated interface for the effective intersection and visualization of genomic region or list sets, thus facilitating their analysis and interpretation.

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1.安装软件

conda install -c bioconda intervene
#This will handle all the dependancies for you.

2.软件使用

intervene venn        -i     bed_fle_directory/*.bed
intervene upset       -i    bed_fle_directory/*.bed
intervene pairwise   -i   bed_fle_directory/*.bed

3.以intervene venn为例子：

intervene venn -i H3K27ac.bed H3K4me3.bed  H3K4me1.bed 

输出结果：

image.png

4.使用帮助

image.png

默认应该是1bp overlap，不过如果想修改可以用bedtools intersect 命令进行修饰。

参考：https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1708-7