bedtools能干啥

bedtools: flexible tools for genome arithmetic and DNA sequence analysis.

usage:    bedtools <subcommand> [options]

The bedtools sub-commands include:

[ Genome arithmetic ]

    intersect     Find overlapping intervals in various ways.

                  求区域之间的交集，可以用来注释peak，计算reads比对到的基因组区域
                  不同样品的peak之间的peak重叠情况。

    window        Find overlapping intervals within a window around an interval.
    closest       Find the closest, potentially non-overlapping interval.

                  寻找最近但可能不重叠的区域

    coverage      Compute the coverage over defined intervals.

                  计算区域覆盖度

    map           Apply a function to a column for each overlapping interval.
    genomecov     Compute the coverage over an entire genome.
    merge         Combine overlapping/nearby intervals into a single interval.

                  合并重叠或相接的区域

    cluster       Cluster (but don't merge) overlapping/nearby intervals.
    complement    Extract intervals _not_ represented by an interval file.

                  获得互补区域

    subtract      Remove intervals based on overlaps b/w two files.

                  计算区域差集

    slop          Adjust the size of intervals.

                  调整区域大小，如获得转录起始位点上下游3 K的区域

    flank         Create new intervals from the flanks of existing intervals.

    sort          Order the intervals in a file.

                  排序，部分命令需要排序过的bed文件

    random        Generate random intervals in a genome.

                  获得随机区域，作为背景集

    shuffle       Randomly redistrubute intervals in a genome.

                  根据给定的bed文件获得随机区域，作为背景集

    sample        Sample random records from file using reservoir sampling.
    spacing       Report the gap lengths between intervals in a file.
    annotate      Annotate coverage of features from multiple files.

[ Multi-way file comparisons ]

    multiinter    Identifies common intervals among multiple interval files.
    unionbedg     Combines coverage intervals from multiple BEDGRAPH files.

[ Paired-end manipulation ]

    pairtobed     Find pairs that overlap intervals in various ways.
    pairtopair    Find pairs that overlap other pairs in various ways.

[ Format conversion ]

    bamtobed      Convert BAM alignments to BED (& other) formats.
    bedtobam      Convert intervals to BAM records.
    bamtofastq    Convert BAM records to FASTQ records.
    bedpetobam    Convert BEDPE intervals to BAM records.
    bed12tobed6   Breaks BED12 intervals into discrete BED6 intervals.

[ Fasta manipulation ]

    getfasta      Use intervals to extract sequences from a FASTA file.

                  提取给定位置的FASTA序列

    maskfasta     Use intervals to mask sequences from a FASTA file.
    nuc           Profile the nucleotide content of intervals in a FASTA file.

[ BAM focused tools ]

    multicov      Counts coverage from multiple BAMs at specific intervals.
    tag           Tag BAM alignments based on overlaps with interval files.

[ Statistical relationships ]

    jaccard       Calculate the Jaccard statistic b/w two sets of intervals.

                  计算数据集相似性

    reldist       Calculate the distribution of relative distances b/w two files.
    fisher        Calculate Fisher statistic b/w two feature files.

[ Miscellaneous tools ]

    overlap       Computes the amount of overlap from two intervals.
    igv           Create an IGV snapshot batch script.

                  用于生成一个脚本，批量捕获IGV截图

    links         Create a HTML page of links to UCSC locations.

    makewindows   Make interval "windows" across a genome.

                  把给定区域划分成指定大小和间隔的小区间 (bin)

    groupby       Group by common cols. & summarize oth. cols. (~ SQL "groupBy")

                  分组结算，不只可以用于bed文件。

    expand        Replicate lines based on lists of values in columns.
    split         Split a file into multiple files with equal records or base pairs.

参考链接可以知道每种功能都是怎么实现的：Bedtools使用