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70 Open 47 Closed
70 Open 47 Closed
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Issues list

brew install bedtools takes forever to run
#170 opened Jul 16, 2024 by zichenzhang04
Multiinter for BEDPE files?
#168 opened Aug 16, 2023 by alistairhockey
Reads doubled when using bamtofastq
#167 opened Jun 27, 2023 by jonathan-bravo
has inconsistent naming convention for record
#166 opened Oct 22, 2022 by CherryX727
Merge delimiter for input file to define how to number columns
#165 opened Aug 12, 2022 by nroak
bedtools makewindows with large genome size
#164 opened Mar 25, 2022 by leegene1992
Including the cigar field when in bamToBed with the -splitD argument
#163 opened Dec 24, 2021 by ndrubins
1
bedtools fisher - how the possible intervals estimated?
#162 opened Oct 13, 2021 by ohdongha
Extract all genes within 5 kb, 10 kb of a genomic range.
#160 opened Jun 12, 2020 by demis001
1
bedtools window produces negative values
#159 opened May 4, 2020 by BenxiaHu
Feature request force strandedness (-s) for complement
#157 opened Oct 31, 2019 by SumNeuron
maskfasta mangles files with mixed line-endings
#156 opened Oct 22, 2019 by bartgrantham
1
Feature request: allow stdin/stdout with maskfasta
#155 opened Oct 21, 2019 by bartgrantham
coverage strand count not accurate compared to samtools for paired end alignment
#154 opened Oct 9, 2019 by mheskett
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 Sep 5, 2019 by burcakotlu
1
Is there a default <GENOME> in bedToBam?
#151 opened Aug 28, 2019 by s-usr
brew installation, update documentation
#147 opened Jul 1, 2019 by evanbiederstedt
1
bedtools_version exception (master branch)
#146 opened May 10, 2019 by chaelir
Bedtools intersect behaviour when crossing 0bp features
#141 opened Jan 17, 2019 by Marmach
getfasta -s not working
#140 opened Dec 5, 2018 by malj390
2
Intersect not working on alignments with MAPQ = 0
#139 opened Oct 24, 2018 by Dave217
[feature] slop without genome file
#138 opened Oct 24, 2018 by shouldsee
coverageBed is not working properly
#137 opened Oct 16, 2018 by khaled-rahman
What does -5 mean in bedtools genomecov?
#136 opened Sep 28, 2018 by Rhine86
2
IntersectBed between a bam and a bed file give different results using or not using -sorted
#135 opened Jul 6, 2018 by qqwang-berkeley
1
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