BEDTools-Teaching: Difference between revisions
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml BEDTools/2.26.0-foss-2016b | ml BEDTools/2.26.0-foss-2016b<br> | ||
bedtools <u>[options]</u><br> | bedtools <u>[options]</u><br> | ||
</div> | </div> |
Revision as of 11:32, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.26.0
Author / Distributor
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 loads the module with
ml BEDTools/2.26.0-foss-2016b
Here is an example of a shell script, sub.sh, to run on at 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
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 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.
Installation
Source code is obtained from BEDTools
System
64-bit Linux