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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: 37:ce3c7f062223
This revision can be installed: True
Times cloned / installed: 21589

Contents of this repository

Name Description Version Minimum Galaxy Version
calculate Fisher statistic between two feature files 2.30.0 16.01
combines coverage intervals from multiple BEDGRAPH files 2.30.0 16.01
converter 2.30.0 16.01
combine overlapping/nearby intervals into a single interval 2.30.0 16.01
cluster overlapping/nearby intervals 2.30.0 16.01
group by common cols and summarize other cols 2.30.0 16.01
find overlapping intervals in various ways 2.30.0 16.01
apply a function to a column for each overlapping interval 2.30.0.2 16.01
counts coverage from multiple BAMs at specific intervals 2.30.0 16.01
tag BAM alignments based on overlaps with interval files 2.30.0 16.01
annotate coverage of features from multiple files 2.30.0 16.01
make interval windows across a genome 2.30.0 16.01
calculate the distribution of relative distances between two files 2.30.0 16.01
find overlapping intervals within a window around an interval 2.30.0 16.01
of features in file B on the features in file A (bedtools coverage) 2.30.0 16.01
use intervals to mask sequences from a FASTA file 2.30.0 16.01
reports the distances between features 2.30.0 16.01
order the intervals 2.30.0 16.01
generate random intervals in a genome 2.30.0 16.01
compute the coverage over an entire genome 2.30.0 16.01
create new intervals from the flanks of existing intervals 2.30.0 16.01
create batch script for taking IGV screenshots 2.30.0 16.01
identifies common intervals among multiple interval files 2.30.0 16.01
find the closest, potentially non-overlapping interval 2.30.0 16.01
computes the amount of overlap from two intervals 2.30.0 16.01
converter 2.30.0 16.01
randomly redistrubute intervals in a genome 2.30.0 16.01
remove intervals based on overlaps 2.30.0 16.01
converter 2.30.0 16.01
profile the nucleotide content of intervals in a FASTA file 2.30.0 16.01
adjust the size of intervals 2.30.0 16.01
Extract intervals not represented by an interval file 2.30.0 16.01
use intervals to extract sequences from a FASTA file 2.30.0 16.01
converter 2.30.0 16.01
calculate the distribution of relative distances 2.30.0 16.01
replicate lines based on lists of values in columns 2.30.0 16.01
create a HTML page of links to UCSC locations 2.30.0 16.01

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