introduction

Bedtools is developed in the Quinlan lab at the University of Utah.
bedtools website

BED format见文末

setup

download bedtools2 from https://github.com/arq5x/bedtools2

make
sudo make install
just type bedtools

install success

bedtools --version #cheak version
bedtools --contact #get more help

download sample files
curl -O https://s3.amazonaws.com/bedtools-tutorials/web/cpg.bed
curl -O https://s3.amazonaws.com/bedtools-tutorials/web/exons.bed
curl -O https://s3.amazonaws.com/bedtools-tutorials/web/gwas.bed
curl -O https://s3.amazonaws.com/bedtools-tutorials/web/hesc.chromHmm.bed

bedtools "intersect"

The intersect command is the workhorse of the bedtools suite. BED/BAM/VCF/GFF

一图看懂系列

基本命令

bedtools intersect -a cpg.bed -b exons.bed > merge.out

只取出cpg.bed和exons.bed重叠的部区域，merge.out文件中CpG与cpg.bed文件中对应的CpG位置可能不同，merget.out ⊆ a.bed

merge.out

输出原始文件中的位置

选项-wa -wb
bedtools intersect -a cpg.bed -b exons.bed -wa > mergeOrigin.out

先算两文件的交集，然后根据交集位置在a文件中取出原始长度
bedtools intersect -a cpg.bed -b exons.bed -wb > mergeOrigin.out
先算两文件的交集，然后根据交集位置在b文件中取出原始长度
bedtools intersect -a cpg.bed -b exons.bed -wa -wb > mergeOrigin.out
先算两文件的交集，然后根据交集位置取出a b文件中包含交集的原始位置

计算overlap的碱基数

选项-wo
bedtools intersect -a cpg.bed -b exons.bed -wo > mergeNum.out

输出a和b文件overlap区域，并且计算出overlap区的碱基数

计算a文件的每个特征区域对应b文件中几个重叠区域

选项-c
bedtools intersect -a cpg.bed -b exons.bed -c > mergeCount.out

提取a文件中与b文件没有重叠的特征区域

选项-v
bedtools intersect -a cpg.bed -b exon.bed -v > mergeDontOverlap.out

设定重叠区域下限

选项-f
bedtools intersect -a cpg.bed -b exon.bed -f 0.5 >merge.out

如果不加-f选项默认的两个区域至少有1 bp的重叠

sorted一下会节省运行时间

选项-sorted
'bedtools intersect -a cpg.bed -b exon.bed -sorted >merge.out'

加入-sorted参数可以加快运行速度，节省时间

文件大小与运行时间统计图

a文件与多个b文件进行intersect

bedtools2支持一个a文件与一个或多个b文件进行intersect操作
bedtools intersect -a exons.bed -b cpg.bed gwas.bed chromHmm.bed -sorted

一个a文件与多个b文件进行intersect时只需要在-b后面跟着几个文件名就可以，其他的选项与上述相同

Brief BED format introduction

include three fields: Required fields, Optional fields, Track line

Required fields

1. chrom
2. chromStart
3. chromEnd

chr1 100000000 100000010
chr1 100000030 100000060
chr2 100010000 100300010

Optional fields

4. name
5. score
6. strand
7. thickStart
8. thickEnd
9. itemRgb
10. blockCount
11. blockSizes
12. blockStarts

Track lines

就是文件开头的简介行