Bedtools tutorial

bedtools: a powerful toolset for genome arithmetic

bedtools Tools are a powerful tool for a wide range of genomic analysis tasks . The most widely used tool enables genome arithmetic ： That is, the set theory on the genome . for example ,bedtools Allow people to start from the widely used genome file format （ Such as BAM、BED、GFF/GTF、VCF） Cross in multiple files of 、 Merge 、 Count 、 Complement and shuffle genome intervals . Although each individual tool is designed to do a relatively simple task （ for example , Intersect with two interval files ）, But through in UNIX Combine multiple on the command line bedtools The operation can carry out quite complex analysis .

Genome annotation file download address
https://genome.ucsc.edu/cgi-bin/hgTables download bed file

bedtools --version #  Version number 
bedtools --contact  #  Help information 

#  Download the test file 
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/genome.txt

###1 bedtools intersect 
##  Calculation overlap intervals
#Tool:    bedtools intersect (aka intersectBed)
#Version: v2.30.0
#Summary: Report overlaps between two feature files.

#Usage:   bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>
# notes ：-b  You can connect multiple files 

#  Show cpg.bed neutralization exons.bed There are overlapping intervals
bedtools intersect -a cpg.bed -b exons.bed
 
#  Show exons.bed neutralization cpg.bed There are overlapping intervals
bedtools intersect -a exons.bed -b cpg.bed 

#  At the same time, the overlapping areas are displayed A、B Original records in the document 
bedtools intersect -a exons.bed -b cpg.bed -wa -wb 

#  Show the base number of overlapping areas 
bedtools intersect -a cpg.bed -b exons.bed -wo

#  Show each one cpg.bed The record in the file is exons.bed Number of overlapping records in the file 
bedtools intersect -a cpg.bed -b exons.bed -c

# cpg.bed There is a disagreement in the document exons.bed whatever intervals Overlapping records 
bedtools intersect -a cpg.bed -b exons.bed -v

bedtools intersect -a cpg.bed -b exons.bed -wo

#  Set threshold , Show cpg.bed in intervals There are at least 50% Sequence sum exons.bed Overlap in 
bedtools intersect -a cpg.bed -b exons.bed -wo -f 0.50

#  Overlapping areas of multiple files 
bedtools intersect -a cpg.bed -b gwas.bed exons.bed 
bedtools intersect -a cpg.bed -b gwas.bed exons.bed -wa -wb -names gwas exon #  Add files label

# sorted Data is added -sorted Parameters , Run faster 
time bedtools intersect -a exons.bed -b cpg.bed gwas.bed -sorted >>/dev/null


###2 bedtools merge
#Tool:    bedtools merge (aka mergeBed)
#Version: v2.30.0
#Summary: Merges overlapping BED/GFF/VCF entries into a single interval.

#Usage:   bedtools merge [OPTIONS] -i <bed/gff/vcf>
# Be careful ：bedtools merge The input file is required to be sorted first 

#  Sort , Input files are sorted by chromosome first , Then sort by starting position .
sort -k1,1 -k2,2n test.bed >test.sorted.bed
#  Show the final " Merge  " Section 
bedtools merge -i exons.bed | head -n 20
#  The calculation leads to every new  " Merge  " The number of overlapping intervals , We will  " Calculation  " First column .
bedtools merge -i exons.bed -c 1 -o count | head -n 20

#  Show all merged into new " Merge  " The second row of the overlapping interval 
bedtools merge -i exons.bed -c 2 -o collapse | head -n 20

#  Merge distance does not exceed 1000 The range of ,
bedtools merge -i exons.bed -d 1000 -c 1 -o count | head -20

#  Merge distance does not exceed 90 Area , Do different operations on the first column and the fourth column respectively 
bedtools merge -i exons.bed -d 90 -c 1,4 -o count,collapse | head -20


###3 bedtools complement 
#Tool:    bedtools complement (aka complementBed)
#Version: v2.30.0
#Summary: Returns the base pair complement of a feature file.

#Usage:   bedtools complement [OPTIONS] -i <bed/gff/vcf> -g <genome>

# notes ：The genome file should tab delimited and structured as follows:
#         <chromName><TAB><chromSize>
# genome.txt in ,exons.bed There is no interval 
bedtools complement -i exons.bed -g genome.txt

###4 bedtools genomecov
#Tool:    bedtools genomecov (aka genomeCoverageBed)
#Version: v2.30.0
#Summary: Compute the coverage of a feature file among a genome.

#Usage: bedtools genomecov [OPTIONS] -i <bed/gff/vcf> -g <genome>
# notes ： Need sorted files 

bedtools genomecov -i exons.bed -g genome.txt
#  Output BEDGRAPH, Calculation intervals Of depth
bedtools genomecov -i exons.bed -g genome.txt -bg | head -20

###5 bedtools jaccard
#Tool:    bedtools jaccard (aka jaccard)
#Version: v2.30.0
#Summary: Calculate Jaccard statistic b/w two feature files.
#     Jaccard is the length of the intersection over the union.
#     Values range from 0 (no intersection) to 1 (self intersection).

#Usage:   bedtools jaccard [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>

#  Calculate similarity 
bedtools jaccard -a cpg.bed -b exons.bed 

###6 bedtools coverage
#Tool:    bedtools coverage (aka coverageBed)
#Version: v2.30.0
#Summary: Returns the depth and breadth of coverage of features from B
#	 on the intervals in A.

#Usage:   bedtools coverage [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>
bedtools coverage  -a cpg.bed -b exons.bed

Reference resources ：

http://quinlanlab.org/tutorials/bedtools/bedtools.html

https://bedtools.readthedocs.io/en/latest/

https://www.jianshu.com/p/f8bbd51b5199​​​​​​​