BEDTools-Teaching

Category

Bioinformatics

Program On

Teaching

Version

2.26.0

Author / Distributor

BEDTools

Description

"The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM." More details are at BEDTools

Running Program

The last version of this application is at /usr/local/apps/eb/BEDTools/2.26.0-foss-2016b

To use this version, please load the module with

ml BEDTools/2.26.0-foss-2016b 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_BEDTools
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BEDTools.%j.out
#SBATCH --error=BEDTools.%j.err

cd $SLURM_SUBMIT_DIR
ml BEDTools/2.26.0-foss-2016b
bedtools [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml BEDTools/2.26.0-foss-2016b 
bedtools -h
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.
    window        Find overlapping intervals within a window around an interval.
    closest       Find the closest, potentially non-overlapping interval.
    coverage      Compute the coverage over defined intervals.
    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.
    cluster       Cluster (but don't merge) overlapping/nearby intervals.
    complement    Extract intervals _not_ represented by an interval file.
    shift         Adjust the position of intervals.
    subtract      Remove intervals based on overlaps b/w two files.
    slop          Adjust the size of intervals.
    flank         Create new intervals from the flanks of existing intervals.
    sort          Order the intervals in a file.
    random        Generate random intervals in a genome.
    shuffle       Randomly redistrubute intervals in a genome.
    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.
    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.
    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.
    links         Create a HTML page of links to UCSC locations.
    makewindows   Make interval "windows" across a genome.
    groupby       Group by common cols. & summarize oth. cols. (~ SQL "groupBy")
    expand        Replicate lines based on lists of values in columns.
    split         Split a file into multiple files with equal records or base pairs.

[ General help ]
    --help        Print this help menu.
    --version     What version of bedtools are you using?.
    --contact     Feature requests, bugs, mailing lists, etc.

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Installation

Source code is obtained from BEDTools

System

64-bit Linux