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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 https://toolshed.g2.bx.psu.edu/repos/iuc/bedtools
Type: unrestricted
Revision: 33:87ee588b3d45
This revision can be installed: True
Times cloned / installed: 10283

Contents of this repository

Name Description Version Minimum Galaxy Version
apply a function to a column for each overlapping interval 2.27.1.2 16.01
use intervals to mask sequences from a FASTA file 2.27.1 16.01
remove intervals based on overlaps 2.27.1 16.01
use intervals to extract sequences from a FASTA file 2.27.1 16.01
annotate coverage of features from multiple files 2.27.1 16.01
reports the distances between features 2.27.1 16.01
cluster overlapping/nearby intervals 2.27.1 16.01
order the intervals 2.27.1 16.01
Extract intervals not represented by an interval file 2.27.1 16.01
generate random intervals in a genome 2.27.1 16.01
computes the amount of overlap from two intervals 2.27.1 16.01
create batch script for taking IGV screenshots 2.27.1 16.01
adjust the size of intervals 2.27.1 16.01
profile the nucleotide content of intervals in a FASTA file 2.27.1 16.01
converter 2.27.1 16.01
combines coverage intervals from multiple BEDGRAPH files 2.27.1 16.01
create a HTML page of links to UCSC locations 2.27.1 16.01
find overlapping intervals in various ways 2.27.1 16.01
compute the coverage over an entire genome 2.27.1 16.01
find overlapping intervals within a window around an interval 2.27.1 16.01
calculate the distribution of relative distances 2.27.1 16.01
converter 2.27.1 16.01
make interval windows across a genome 2.27.1 16.01
counts coverage from multiple BAMs at specific intervals 2.27.1 16.01
of features in file B on the features in file A (bedtools coverage) 2.27.1 16.01
group by common cols and summarize other cols 2.27.1 16.01
calculate Fisher statistic between two feature files 2.27.1 16.01
calculate the distribution of relative distances between two files 2.27.1 16.01
2.27.1 16.01
create new intervals from the flanks of existing intervals 2.27.1 16.01
converter 2.27.1 16.01
randomly redistrubute intervals in a genome 2.27.1 16.01
tag BAM alignments based on overlaps with interval files 2.27.1 16.01
replicate lines based on lists of values in columns 2.27.1 16.01
find the closest, potentially non-overlapping interval 2.27.1 16.01
converter 2.27.1 16.01
combine overlapping/nearby intervals into a single interval 2.27.1 16.01
identifies common intervals among multiple interval files 2.27.1 16.01

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