BenLangmead/bowtie

Issues

• bowtie for short reads

  #141 opened 4 months ago by alessandromacc
  1

• Compatibility of Bowtie1 (v1.2.0 or later) with Tophat2

  #138 opened a year ago by rason81
  1

• bowtie alignmnet produces sam bam files sizes for different fastq files

  #140 opened 6 months ago by deepthi-omics
  0

• secondary alignment flag

  #139 opened a year ago by adthrasher
  0

• Install bowtie

  #110 opened 3 years ago by paolabc
  1

• Is there an equivalent of "Bowtie2 --very-sensitive" for Bowtie1 [suggested label = Question]

  #137 opened 2 years ago by AndreaMariani-AM
  0

• Cline paired 2 (fw:1, sam:1) test aborted with -Wp,-D_GLIBCXX_ASSERTIONS

  #136 opened 2 years ago by junaruga
  4

• Some reference entries show up as duplicates

  #135 opened 2 years ago by DeadlineWasYesterday
  1

• Questions about tracking the history of building index

  #134 opened 2 years ago by Youpu-Chen
  0

• -m setting not outputting a sam file with an -NH tag

  #133 opened 2 years ago by elayton13
  0

• Bowtie not mapping 100%

  #130 opened 3 years ago by Stakaitis
  1

• Error: reads file does not look like a FASTQ file

  #129 opened 3 years ago by amitjavilaventura
  2

• Bowtie no longer works with updated versions of tbb

  #128 opened 3 years ago by ryandward
  0

• bowtie-1.2.2: ebwt.h:865:44: error: cannot convert 'TIndexOffU* const' {aka 'long unsigned int* const'} to 'uint32_t*' {aka 'unsigned int*'} in return

  #90 opened 3 years ago by mmokrejs
  3

• bowtie reports incorrect result when using bowtie2 index

  #103 opened 3 years ago by qifei9
  3

• bowtie mapping with fasta input - segmentation fault.

  #86 opened 3 years ago by mortunco
  1

• bowtie with recent SeqAn

  #93 opened 3 years ago by mestia
  3

• Please update scripts using python to python3

  #97 opened 3 years ago by mestia
  1

• Renaming the v1.2.3 src archive to "bowtie-1.2.3-src.zip"?

  #101 opened 3 years ago by junaruga
  4

• Axolotl genome index building with Bowtie 1.2.3

  #96 opened 3 years ago by Gil-marquez
  3

• s390x/ppc64le: bt2_locks.h: Error: Unrecognized opcode: `pause'

  #114 opened 3 years ago by junaruga
  6

• What is the sense of third_party/cpuid.h

  #117 opened 3 years ago by tillea
  2

• Bowtie hangs when running on very large genomes

  #124 opened 3 years ago by ferayd
  8

• -M option reports the wrong number of reads processed

  #125 opened 3 years ago by dominik-handler
  2

• XM:i SAM Optional field ... seems like hits + 1 for all hits?

  #127 opened 3 years ago by MikeAxtell
  3

• bowtie install error on Apple M1

  #122 opened 3 years ago by hidvegin
  1

• problem with option -n and -l

  #126 opened 3 years ago by mewu3
  0

• Bowtie: "Floating point exception: 8"

  #118 opened 4 years ago by marcopann
  1

• Mismatch flag

  #123 opened 3 years ago by KONeill872
  0

• Migrate Travis CI by May 31, 2021

  #120 opened 4 years ago by junaruga
  0

• bowtie 1.3.0 generated sam files error

  #119 opened 4 years ago by hidvegin
  11

• Missing newlines in --max and --un output files

  #100 opened 4 years ago by ferayd
  18

• DeprecationWarning: the imp module is deprecated

  #115 opened 4 years ago by junaruga
  2

• Invalid double quote character is used in the code

  #104 opened 4 years ago by junaruga
  3

• SeqAn license info is not enough?

  #106 opened 4 years ago by junaruga
  4

• Unmapped reads not suppressed using --no-unal and possibly wrong stderr stats

  #107 opened 4 years ago by bepoli
  2

• Can bowtie accepts genomes higher than 3Gb for aligning?

  #113 opened 4 years ago by AG-Run
  0

• Special characters in manual

  #112 opened 4 years ago by BenLangmead
  0

• bowtie-build --debug --sanity crashes

  #111 opened 4 years ago by BenLangmead
  0

• Code clean up?

  #109 opened 5 years ago by mathog
  4

• bowtie-align-l-debug fail

  #108 opened 5 years ago by bensonlew
  0

• Maximum mismatches allowed is 2

  #89 opened 5 years ago by johanzi
  3

• Get decoded content of index files

  #98 opened 5 years ago by lazovicff
  1

• The -m option only results in some "many mapped" reads being supressed

  #94 opened 5 years ago by Riptides
  0

• Bowtie clips read before matching

  #92 opened 5 years ago by ferayd
  4

• Re-open issue: invalid fastq files produced using --un #8

  #88 opened 6 years ago by elenichri
  4

• bowtie installation

  #83 opened 7 years ago by VizeacoumarLab
  1

• Extremely low mapping rate using D. melanogaster, Flybase, r5.22 genome index

  #91 opened 6 years ago by ruochenj
  1

• bowtie fails to build on Debian testing/gcc-8

  #87 opened 6 years ago by mestia
  4

• r

  #85 opened 6 years ago by AustinGutierrez
  0