Installation and use of Bedtools

1) Installation

Bedtools offers 3 mounting options

• Download source code from Google code to install
• Install using the package management tools in the system, such as Yum under Cnetos, Apt-get under Ubuntu, homebrew under Mac
• Download the source code from GitHub for installation

Since you can't access Google code and want to compile the installation, download the latest version from GitHub: HTTPS://GITHUB.COM/ARQ5X/BEDTOOLS2

Download the v2.25.0 version of the source code for installation

wget https://github.com/arq5x/bedtools2/archive/v2.25.0.tar.gztar XZVF v2. 25.0 CD BEDTOOLS2-2.25. 0/makeCD bin/export PATH= $PWD: $PATH

2) Use

Intersect: Ask for the intersection of two intervals, the input file can be BED,GFF,VCF

Prepare two test files,

Cpg.bed, the contents of which are

Chr12070cpg_1chr1100120cpg_2chr1150250cpg_3

Exon.bed, the contents of which are

Chr11040exon_1chr15060exon_2chr1130180exon_3chr1200280exon_4

Using the default parameters, please overlap the file, run

Bedtools intersect-a cpg.bed-  b exon.bed

Result is

Chr12040cpg_1chr15060cpg_1chr1150180cpg_3chr1200250cpg_3

As you can see, by default only the area of overlap in a is output

Add the-wa parameter and run it again

Bedtools intersect-a cpg.bed-  b Exon.bed-wa

The result is:

Chr12070cpg_1chr12070cpg_1chr1150250cpg_3chr1150250cpg_3

As can be seen, with the-wa parameter, as long as the area in A and B in the area has a intersection, the output, and overlap several times, the output several times

Add-WB parameter, run

Bedtools intersect-a cpg.bed-  b EXON.BED-WB

The result is:

Chr12040cpg_1chr11040exon_1chr15060cpg_1chr15060exon_2chr1150180cpg_3chr1130180exon_3chr1200250cpg_ 3chr1200280exon_4

As you can see, with the-WB parameter, the entire range in B is output in addition to the overlap area in output a.

Add-wa,-WB parameters, run again

Bedtools intersect-a cpg.bed-  b EXON.BED-WA-WB

The result is:

Chr12070cpg_1chr11040exon_1chr12070cpg_1chr15060exon_2chr1150250cpg_3chr1130180exon_3chr1150250cpg_ 3chr1200280exon_4

As you can see, adding the-wa and-WB parameters at the same time will output the overlap area in pairs

-C parameter, count the number of each region and Boverlap in a

Bedtools intersect-a cpg.bed-  b exon.bed-c

The result is:

Chr12070cpg_12chr1100120cpg_20chr1150250cpg_32

-V parameter: only outputs a zone with no boverlap in a

Bedtools intersect-a cpg.bed-  b exon.bed-v

The result is:

Chr1100120cpg_2

As you can see, as long as the overlap with B is not output.

　　

　

　　

　　

　　

　　

　　

　　

　　

　　

　　

Installation and use of Bedtools