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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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`brew install bedtools` takes forever to run
#170
zichenzhang04
opened
1 month ago
0
bedtools getFASTA is not converting a whole BED file
#169
mbroad1
closed
5 months ago
10
Multiinter for BEDPE files?
#168
alistairhockey
opened
1 year ago
0
Reads doubled when using `bamtofastq`
#167
jonathan-bravo
opened
1 year ago
0
has inconsistent naming convention for record
#166
CherryX727
opened
1 year ago
0
Merge delimiter for input file to define how to number columns
#165
nroak
opened
2 years ago
0
bedtools makewindows with large genome size
#164
leegene1992
opened
2 years ago
0
Including the cigar field when in bamToBed with the -splitD argument
#163
ndrubins
opened
2 years ago
1
bedtools fisher - how the possible intervals estimated?
#162
ohdongha
opened
2 years ago
0
Minor fix to parameter default listed
#161
bergeycm
opened
3 years ago
0
Extract all genes within 5 kb, 10 kb of a genomic range.
#160
demis001
opened
4 years ago
1
bedtools window produces negative values
#159
BenxiaHu
opened
4 years ago
0
Bedtools getfasta and ORF from a blastX run
#158
StromTroopers
closed
4 years ago
0
Feature request force strandedness (`-s`) for complement
#157
SumNeuron
opened
4 years ago
0
maskfasta mangles files with mixed line-endings
#156
bartgrantham
opened
4 years ago
1
Feature request: allow stdin/stdout with maskfasta
#155
bartgrantham
opened
4 years ago
0
coverage strand count not accurate compared to samtools for paired end alignment
#154
mheskett
opened
4 years ago
0
bedtools jaccard segmentation fault
#153
Adrien-Evo
closed
4 years ago
2
NotImplementedError: "intersectBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method.
#152
burcakotlu
opened
4 years ago
1
Is there a default <GENOME> in bedToBam?
#151
s-usr
opened
5 years ago
0
getfasta coordinates error?
#150
jfass
closed
5 years ago
1
Issue in merge (0-based or 1-based) [v2.28.0]
#149
daramism
closed
5 years ago
1
inaccurate counts with bedtools intersect -split and -f
#148
benslack19
closed
5 years ago
1
brew installation, update documentation
#147
evanbiederstedt
opened
5 years ago
1
bedtools_version exception (master branch)
#146
chaelir
opened
5 years ago
0
bedtools intersect -v fails with self
#145
endrebak
closed
5 years ago
1
bedtools complement hangs when using -i <(cmd)
#144
outpaddling
closed
5 years ago
1
fixed chr with chr1
#143
Nazeeefa
closed
5 years ago
0
Bedtools subtract misses whole chromosomes when -sorted -g ref.dict
#142
nh13
closed
5 years ago
1
Bedtools intersect behaviour when crossing 0bp features
#141
Marmach
opened
5 years ago
0
getfasta -s not working
#140
malj390
opened
5 years ago
2
Intersect not working on alignments with MAPQ = 0
#139
Dave217
opened
5 years ago
0
[feature] slop without genome file
#138
shouldsee
opened
5 years ago
0
coverageBed is not working properly
#137
khaled-rahman
opened
5 years ago
0
What does -5 mean in bedtools genomecov?
#136
Rhine86
opened
5 years ago
2
IntersectBed between a bam and a bed file give different results using or not using -sorted
#135
qqwang-berkeley
opened
6 years ago
1
ERROR: Sort order was unspecified, and file <my.bam> is not sorted lexicographically.
#134
hanjunjeon
opened
6 years ago
0
Important! bedtools coverage [2.25.0]
#133
hmyh1202
opened
6 years ago
0
bedtools: unionBedGraphs.cpp:99 error
#132
xmzhuo
opened
6 years ago
2
bedtools coverage -sortout
#131
akukalev
opened
6 years ago
0
Some issues with help menu on sample and spacing
#130
mayurapatwardhan
opened
6 years ago
0
Error using genomecov
#129
sengoku93
closed
6 years ago
1
ERROR: LeakSanitizer: detected memory leaks with bedtools intersect
#128
blaiseli
opened
6 years ago
0
BAM to BEDPE
#127
hmyh1202
opened
6 years ago
0
Piping BAM file between bedtools commands
#126
jma1991
closed
6 years ago
1
coordinate system query
#125
prasundutta87
opened
6 years ago
0
groupBy & coverageBed (v 2.26.0) confusing results
#124
itsvenu
closed
6 years ago
1
bedSort fails for 0 length features
#123
bernt-matthias
opened
6 years ago
1
intersect bam files error
#122
parvathisudha
opened
6 years ago
0
Online documentation not up-to-date
#121
blaiseli
closed
7 years ago
1
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