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Repository bedtools
Name: bedtools
Owner: iuc
Synopsis: bedtools is a powerful toolset for genome arithmetic
Collectively, the bedtools utilities are a swiss-army knife of
tools for a wide-range of genomics analysis tasks. The most widely-used tools enable
genome arithmetic: that is, set theory on the genome. For example, bedtools allows
one to intersect, merge, count, complement, and shuffle genomic intervals from multiple
files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While
each individual tool is designed to do a relatively simple task (e.g., intersect
two interval files), quite sophisticated analyses can be conducted by combining
multiple bedtools operations.
Clone this repository: hg clone
Type: unrestricted
Revision: 30:db1841942d2b
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Contents of this repository

Name Description Version Minimum Galaxy Version
apply a function to a column for each overlapping interval 16.01
use intervals to mask sequences from a FASTA file 16.01
remove intervals based on overlaps 16.01
use intervals to extract sequences from a FASTA file 16.01
annotate coverage of features from multiple files 16.01
reports the distances between features 16.01
cluster overlapping/nearby intervals 16.01
order the intervals 16.01
Extract intervals not represented by an interval file 16.01
generate random intervals in a genome 16.01
computes the amount of overlap from two intervals 16.01
create batch script for taking IGV screenshots 16.01
adjust the size of intervals 16.01
profile the nucleotide content of intervals in a FASTA file 16.01
converter 16.01
combines coverage intervals from multiple BEDGRAPH files 16.01
create a HTML page of links to UCSC locations 16.01
find overlapping intervals in various ways 16.01
compute the coverage over an entire genome 16.01
find overlapping intervals within a window around an interval 16.01
calculate the distribution of relative distances 16.01
converter 16.01
make interval windows across a genome 16.01
counts coverage from multiple BAMs at specific intervals 16.01
of features in file B on the features in file A (bedtools coverage) 16.01
group by common cols and summarize other cols 16.01
calculate Fisher statistic between two feature files 16.01
calculate the distribution of relative distances between two files 16.01 16.01
create new intervals from the flanks of existing intervals 16.01
converter 16.01
randomly redistrubute intervals in a genome 16.01
tag BAM alignments based on overlaps with interval files 16.01
replicate lines based on lists of values in columns 16.01
find the closest, potentially non-overlapping interval 16.01
converter 16.01
combine overlapping/nearby intervals into a single interval 16.01
identifies common intervals among multiple interval files 16.01

Text Manipulation - Tools for manipulating data
Genomic Interval Operations - Tools for operating on genomic intervals