bedtools使用教程

bedtools: a powerful toolset for genome arithmetic

bedtools工具是用于广泛的基因组学分析任务的一把利器。最广泛使用的工具能够实现基因组算术：即基因组上的集合理论。例如，bedtools允许人们从广泛使用的基因组文件格式（如BAM、BED、GFF/GTF、VCF）的多个文件中交叉、合并、计数、互补和洗牌基因组区间。虽然每个单独的工具被设计用来做一个相对简单的任务（例如，与两个区间文件相交），但通过在UNIX命令行上结合多个bedtools操作可以进行相当复杂的分析。

基因组注释文件下载地址
https://genome.ucsc.edu/cgi-bin/hgTables 下载bed文件

bedtools --version # 版本号
bedtools --contact  # 帮助信息

# 下载测试文件
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 
## 计算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>
#注：-b 可以接多个文件

# 显示cpg.bed中和exons.bed有重叠的intervals
bedtools intersect -a cpg.bed -b exons.bed
 
# 显示exons.bed中和cpg.bed有重叠的intervals
bedtools intersect -a exons.bed -b cpg.bed 

# 同时显示重叠区域的A、B文件中的原始记录
bedtools intersect -a exons.bed -b cpg.bed -wa -wb 

# 显示重叠区域的碱基数
bedtools intersect -a cpg.bed -b exons.bed -wo

# 显示每一个cpg.bed文件中的记录在exons.bed文件中的重叠记录数
bedtools intersect -a cpg.bed -b exons.bed -c

# cpg.bed文件中不和exons.bed任何intervals重叠的记录
bedtools intersect -a cpg.bed -b exons.bed -v

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

# 设定阈值，显示cpg.bed中intervals至少有50%序列和exons.bed中的重叠
bedtools intersect -a cpg.bed -b exons.bed -wo -f 0.50

# 多个文件的重叠区域
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 # 加上文件label

# sorted数据通过加-sorted参数，运行速度更快
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>
#注意：bedtools merge要求输入文件先排序

# 排序，输入文件先按染色体排序，然后按起始位置排序。
sort -k1,1 -k2,2n test.bed >test.sorted.bed
# 显示最终的"合并 "区间
bedtools merge -i exons.bed | head -n 20
# 在计算导致每个新的 "合并 "区间的重叠区间的数量时，我们将 "计算 "第一列。
bedtools merge -i exons.bed -c 1 -o count | head -n 20

# 显示所有合并成新的"合并 "区间的重叠区间的第二行
bedtools merge -i exons.bed -c 2 -o collapse | head -n 20

# 合并距离不超过1000的区间，
bedtools merge -i exons.bed -d 1000 -c 1 -o count | head -20

# 合并距离不超过90区域，分别对第一列和第四列做不同的操作
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>

#注：The genome file should tab delimited and structured as follows:
#         <chromName><TAB><chromSize>
# genome.txt中，exons.bed没有的区间
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>
#注：需要排序好的文件

bedtools genomecov -i exons.bed -g genome.txt
# 输出BEDGRAPH,计算intervals的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>

# 计算相似度
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

参考：

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

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

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