Issues

• brew install bedtools takes forever to run

  arq5x/bedtools#170 · Filter by author zichenzhang04 opened on Jul 16, 2024

• Multiinter for BEDPE files?

  arq5x/bedtools#168 · Filter by author alistairhockey opened on Aug 16, 2023

• Reads doubled when using bamtofastq

  arq5x/bedtools#167 · Filter by author jonathan-bravo opened on Jun 27, 2023

• has inconsistent naming convention for record

  arq5x/bedtools#166 · Filter by author CherryX727 opened on Oct 22, 2022

• Merge delimiter for input file to define how to number columns

  arq5x/bedtools#165 · Filter by author nroak opened on Aug 12, 2022

• bedtools makewindows with large genome size

  arq5x/bedtools#164 · Filter by author leegene1992 opened on Mar 25, 2022

• Including the cigar field when in bamToBed with the -splitD argument

  arq5x/bedtools#163 · Filter by author ndrubins opened on Dec 24, 2021
  1

• bedtools fisher - how the possible intervals estimated?

  arq5x/bedtools#162 · Filter by author ohdongha opened on Oct 13, 2021

• Extract all genes within 5 kb, 10 kb of a genomic range.

  arq5x/bedtools#160 · Filter by author demis001 opened on Jun 12, 2020
  1

• bedtools window produces negative values

  arq5x/bedtools#159 · Filter by author BenxiaHu opened on May 4, 2020

• Feature request force strandedness (-s) for complement

  arq5x/bedtools#157 · Filter by author SumNeuron opened on Oct 31, 2019

• maskfasta mangles files with mixed line-endings

  arq5x/bedtools#156 · Filter by author bartgrantham opened on Oct 22, 2019
  1

• Feature request: allow stdin/stdout with maskfasta

  arq5x/bedtools#155 · Filter by author bartgrantham opened on Oct 21, 2019

• coverage strand count not accurate compared to samtools for paired end alignment

  arq5x/bedtools#154 · Filter by author mheskett opened on Oct 9, 2019

• 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.

  arq5x/bedtools#152 · Filter by author burcakotlu opened on Sep 5, 2019
  1

• Is there a default <GENOME> in bedToBam?

  arq5x/bedtools#151 · Filter by author s-usr opened on Aug 28, 2019

• brew installation, update documentation

  arq5x/bedtools#147 · Filter by author evanbiederstedt opened on Jul 1, 2019
  1

• bedtools_version exception (master branch)

  arq5x/bedtools#146 · Filter by author chaelir opened on May 10, 2019

• Bedtools intersect behaviour when crossing 0bp features

  arq5x/bedtools#141 · Filter by author Marmach opened on Jan 17, 2019

• getfasta -s not working

  arq5x/bedtools#140 · Filter by author malj390 opened on Dec 5, 2018
  2

• Intersect not working on alignments with MAPQ = 0

  arq5x/bedtools#139 · Filter by author Dave217 opened on Oct 24, 2018

• [feature] slop without genome file

  arq5x/bedtools#138 · Filter by author shouldsee opened on Oct 24, 2018

• coverageBed is not working properly

  arq5x/bedtools#137 · Filter by author khaled-rahman opened on Oct 16, 2018

• What does -5 mean in bedtools genomecov?

  arq5x/bedtools#136 · Filter by author Rhine86 opened on Sep 28, 2018
  2

• IntersectBed between a bam and a bed file give different results using or not using -sorted

  arq5x/bedtools#135 · Filter by author qqwang-berkeley opened on Jul 6, 2018
  1