sestaton/Transposome

Issues

• repeat_database for complex metagenomics data?

  #46 opened a year ago by mmpust
  1

• A error about convert.

  #42 opened 2 years ago by Jerrywang-evo
  3

• [mgblast] FATAL ERROR: CoreLib [001.000] Failed to allocate 67108864 bytes

  #44 opened 2 years ago by QianghuiZhu
  1

• Issue with make test - Blast and UnionFinder

  #45 opened 3 years ago by cahende
  1

• Error at the beginning of Transposome

  #43 opened 4 years ago by KristinaGagalova
  1

• formatdb and mgblast dependencies

  #36 opened 8 years ago by abretaud
  4

• Louvain 'community' failed

  #41 opened 6 years ago by aleksberic
  4

• Installation: make test

  #39 opened 6 years ago by qsantana
  4

• Louvain 'community' failed.

  #28 opened 9 years ago by etwatson
  11

• Reads not found in merge_clusters method

  #40 opened 7 years ago by sestaton
  1

• GenomeFrac is too high

  #34 opened 7 years ago by etwatson
  7

• How to format the repeat database for Transposome analysis

  #37 opened 7 years ago by pyrevo
  14

• Reformat RepeatModeler-based library

  #38 opened 7 years ago by davidecarlson
  6

• PairFinder error

  #35 opened 8 years ago by PolinaN
  7

• Input allvall_blast.bln file read as empty by PairFinder

  #32 opened 8 years ago by eagerowl120
  15

• Can't locate error. Somewhere around a shell script at the beginning of Blast?

  #30 opened 9 years ago by RubyDrus
  13

• Library of custom repeats without superfamily name

  #33 opened 9 years ago by etwatson
  5

• Running transposome with contigs instead of reads

  #31 opened 9 years ago by tlorin
  2

• Clarify what are singleton repeats in log

  #29 opened 9 years ago by sestaton
  0

• sequence number not passing type constriaint in blast method

  #25 opened 9 years ago by sestaton
  2

• make_clusters killed

  #27 opened 9 years ago by etwatson
  2

• parse_blast format error

  #26 opened 9 years ago by etwatson
  3

• DBM::Deep error

  #24 opened 9 years ago by etwatson
  13

• empty clusters written to cluster file

  #22 opened 9 years ago by sestaton
  0

• log cluster number before annotation step completes

  #23 opened 9 years ago by sestaton
  1

• Bug in PairFinder method "can't get sector..."

  #21 opened 9 years ago by sestaton
  1

• some methods are logging twice

  #20 opened 10 years ago by sestaton
  1

• remove merge_threshold option from configuration

  #19 opened 10 years ago by sestaton
  1

• remove cpus and sequence number options from configuration file

  #18 opened 10 years ago by sestaton
  1

• Make annotation methods take a hash instead of a list of arguments

  #15 opened 10 years ago by sestaton
  1

• Feature request: Add options to only do certain steps of the analysis

  #16 opened 10 years ago by sestaton
  1

• Add plot to wiki showing relationship of genome coverage and run time

  #17 opened 10 years ago by sestaton
  0

• Fasta files not found after clustering

  #14 opened 10 years ago by sestaton
  2

• Index files should be written to the output directory

  #13 opened 10 years ago by sestaton
  2

• ERROR: cannot find 'formatdb'

  #12 opened 10 years ago by sestaton
  1

• Rework annotation mapping methods

  #11 opened 10 years ago by sestaton
  1

• report run parameters in log

  #10 opened 10 years ago by sestaton
  1

• Can't locate object method "new_with_options"

  #9 opened 10 years ago by gabyrech
  4

• Add CLI tutorial to wiki

  #6 opened 10 years ago by sestaton
  1

• Add support for fastq input to self comparison method

  #8 opened 10 years ago by sestaton
  1

• check if blast completed successfully before clustering

  #7 opened 10 years ago by sestaton
  1

• Check for existence of repeat database and sequence file

  #4 opened 11 years ago by sestaton
  2

• Add singleton repeat sequences to annotation summary

  #5 opened 11 years ago by sestaton
  1

• make portable file paths

  #3 opened 11 years ago by sestaton
  1

• Check for local or custom installation

  #2 opened 11 years ago by sestaton
  1