Issues
- 0
`brew install bedtools` takes forever to run
#170 opened by zichenzhang04 - 1
brew installation, update documentation
#147 opened by evanbiederstedt - 10
bedtools getFASTA is not converting a whole BED file
#169 opened by mbroad1 - 0
Multiinter for BEDPE files?
#168 opened by alistairhockey - 0
Reads doubled when using `bamtofastq`
#167 opened by jonathan-bravo - 1
- 0
has inconsistent naming convention for record
#166 opened by CherryX727 - 2
What does -5 mean in bedtools genomecov?
#136 opened by Rhine86 - 0
- 0
bedtools makewindows with large genome size
#164 opened by leegene1992 - 0
- 1
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 opened by burcakotlu - 1
Extract all genes within 5 kb, 10 kb of a genomic range.
#160 opened by demis001 - 0
bedtools window produces negative values
#159 opened by BenxiaHu - 2
getfasta -s not working
#140 opened by malj390 - 2
bedtools jaccard segmentation fault
#153 opened by Adrien-Evo - 0
Bedtools getfasta and ORF from a blastX run
#158 opened by StromTroopers - 0
- 1
maskfasta mangles files with mixed line-endings
#156 opened by bartgrantham - 0
- 0
coverage strand count not accurate compared to samtools for paired end alignment
#154 opened by mheskett - 0
Is there a default <GENOME> in bedToBam?
#151 opened by s-usr - 1
getfasta coordinates error?
#150 opened by jfass - 1
Issue in merge (0-based or 1-based) [v2.28.0]
#149 opened by daramism - 1
- 0
bedtools_version exception (master branch)
#146 opened by chaelir - 1
bedtools complement hangs when using -i <(cmd)
#144 opened by outpaddling - 1
bedtools intersect -v fails with self
#145 opened by endrebak - 1
- 2
bedtools: unionBedGraphs.cpp:99 error
#132 opened by xmzhuo - 0
- 0
Intersect not working on alignments with MAPQ = 0
#139 opened by Dave217 - 0
[feature] slop without genome file
#138 opened by shouldsee - 0
coverageBed is not working properly
#137 opened by khaled-rahman - 1
IntersectBed between a bam and a bed file give different results using or not using -sorted
#135 opened by qqwang-berkeley - 0
ERROR: Sort order was unspecified, and file <my.bam> is not sorted lexicographically.
#134 opened by hanjunjeon - 0
Important! bedtools coverage [2.25.0]
#133 opened by hmyh1202 - 0
bedtools coverage -sortout
#131 opened by akukalev - 0
Some issues with help menu on sample and spacing
#130 opened by mayurapatwardhan - 1
Error using genomecov
#129 opened by sengoku93 - 0
- 0
BAM to BEDPE
#127 opened by hmyh1202 - 1
Piping BAM file between bedtools commands
#126 opened by jma1991 - 0
coordinate system query
#125 opened by prasundutta87 - 1
groupBy & coverageBed (v 2.26.0) confusing results
#124 opened by itsvenu - 1
bedSort fails for 0 length features
#123 opened by bernt-matthias - 0
intersect bam files error
#122 opened by parvathisudha - 1
bedtools sort -faidx option is undocumented
#119 opened by tedtoal - 1
Online documentation not up-to-date
#121 opened by blaiseli - 0
bedtools intersect problem
#120 opened