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arq5x
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bedtools
A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
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bedtools intersect problem
#120
ghost
opened
7 years ago
0
bedtools sort -faidx option is undocumented
#119
tedtoal
closed
7 years ago
1
Confused about flank, getfasta, sort, and strands
#118
olgabot
opened
8 years ago
11
Request: Add minimum mapping quality to genomecov
#117
tantrev
closed
8 years ago
1
Multitple ops in groupby
#116
pthiru
opened
8 years ago
0
support for MAF files
#115
duartemolha
closed
8 years ago
2
unionbedg
#114
flay
opened
8 years ago
6
Help is not printed
#113
dariober
opened
8 years ago
1
bug: ragged output from intersect of bed3 and bed4
#112
dwaggott
closed
8 years ago
0
annotating vcf with intersect
#111
dwaggott
closed
8 years ago
0
Feature request - intersect minimal fraction in either interval
#110
michael-imbeault
closed
9 years ago
0
Sort order of BAM and BED files are different so cannot use -sorted option in bedtools coverage
#109
jma1991
closed
9 years ago
20
bedtools coverage -d off-by-one?
#108
rolfschr
closed
9 years ago
1
tools with -sorted input should default to sorted output
#107
brentp
closed
9 years ago
0
bedtools genomecov
#106
dashainparis
opened
9 years ago
0
groupBy retaining sort order on distinct operation
#105
duartemolha
opened
9 years ago
0
Parsing BED file
#104
guillermomarco
opened
9 years ago
3
bedtools expects "chr1" in VCF where reference data uses "1"
#103
aksarkar
closed
8 years ago
0
Update intersect.rst
#102
ghost
closed
1 month ago
0
Issue with overlap length in intersect -split?
#101
ghost
opened
10 years ago
0
Fixed small error in example output of mergeBed -d
#100
bergeycm
closed
8 years ago
1
Title correction on -counts part
#99
Guitss
closed
10 years ago
0
Update cluster.rst
#98
rchikhi
closed
10 years ago
3
Update installation.rst
#97
arjanvandervelde
closed
10 years ago
1
Potential bug causing segfault dump in makewindows
#96
yarden
opened
10 years ago
2
Update window.rst
#95
cbirger
closed
10 years ago
1
Update subtract.rst
#94
cbirger
closed
10 years ago
1
fix description of option -Sm
#93
dangenet
closed
10 years ago
1
Enhancement: subtractBed: Add switch to allow -a file to be read in memory and -b from disk
#92
ghuls
opened
10 years ago
1
Update merge.rst
#91
ecwooten
closed
11 years ago
1
VCF output truncated, if blank line follows header
#90
daler
opened
11 years ago
2
Fix output format of optional BED fields
#89
kcha
closed
10 years ago
1
Blank BED files throw an error
#88
jsilter
opened
11 years ago
1
Update intersect.rst
#87
bergeycm
closed
11 years ago
1
Update window.rst
#86
jsilter
closed
11 years ago
1
Invalid -f Argument in windowBed
#85
duartemolha
opened
11 years ago
4
Update merge.rst
#84
kzarns
opened
11 years ago
2
added mouse.mm10.genome
#83
theoryno3
closed
11 years ago
1
Update slop.rst
#82
wac
closed
11 years ago
0
Update quick-start.rst
#81
daler
closed
11 years ago
1
Update quick-start.rst
#80
daler
closed
11 years ago
0
Change the actual default delim for merge (it's ";" not ",")
#79
nachocab
closed
11 years ago
1
Does bedtools handle the ##FASTA tag in gff files?
#78
ctSkennerton
closed
11 years ago
3
bedtools coverage should have a -sorted option
#77
brentp
opened
11 years ago
3
ENH: shuffle intervals to non-overlapping locations.
#76
brentp
closed
11 years ago
2
Update merge.rst
#75
lbthrice
closed
11 years ago
1
ENH: shuffle within a window or distance
#74
brentp
opened
11 years ago
0
ENH: implement new tool bedtools sample
#73
brentp
opened
11 years ago
0
Intersect library fragments and not alignment in multibamcov
#72
dawe
opened
11 years ago
1
Add -f option to window
#71
arq5x
opened
11 years ago
0
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