arq5x bedtools issues - Githubissues

arq5x / bedtools

A powerful toolset for genome arithmetic.

http://code.google.com/p/bedtools/

GNU General Public License v2.0

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issues

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`brew install bedtools` takes forever to run

#170 zichenzhang04 opened 4 months ago
0
bedtools getFASTA is not converting a whole BED file

#169 mbroad1 closed 8 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 2 years 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 3 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 5 years ago
0
Feature request force strandedness (`-s`) for complement

#157 SumNeuron opened 5 years ago
0
maskfasta mangles files with mixed line-endings

#156 bartgrantham opened 5 years ago
1
Feature request: allow stdin/stdout with maskfasta

#155 bartgrantham opened 5 years ago
0
coverage strand count not accurate compared to samtools for paired end alignment

#154 mheskett opened 5 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 5 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 6 years ago
0
[feature] slop without genome file

#138 shouldsee opened 6 years ago
0
coverageBed is not working properly

#137 khaled-rahman opened 6 years ago
0
What does -5 mean in bedtools genomecov?

#136 Rhine86 opened 6 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 7 years ago
1
coordinate system query

#125 prasundutta87 opened 7 years ago
0
groupBy & coverageBed (v 2.26.0) confusing results

#124 itsvenu closed 7 years ago
1
bedSort fails for 0 length features

#123 bernt-matthias opened 7 years ago
1
intersect bam files error

#122 parvathisudha opened 7 years ago
0
Online documentation not up-to-date

#121 blaiseli closed 7 years ago
1