sestaton/tephra

Issues

• Question about how to run Tephra correctly?

  #51 opened 9 months ago by CSU-KangHu
  6

• Report bugs

  #50 opened 2 years ago by naishikawa
  3

• Make test errors

  #49 opened 2 years ago by pasviber
  9

• INSTALL ERROR

  #26 opened 3 years ago by yangxiaofeill
  6

• issue with gene file

  #48 opened 4 years ago by jcerca
  3

• Problem with install

  #47 opened 4 years ago by bioinformaticaInta
  2

• Singularity yml parsing error

  #43 opened 5 years ago by eganko
  15

• singularity container doesn't contain perldoc

  #44 opened 4 years ago by nhartwic
  2

• Report a bug

  #45 opened 4 years ago by altingia
  2

• sh: 0: Illegal option -j

  #46 opened 4 years ago by jguhlin
  5

• Error running tephra age command

  #38 opened 5 years ago by davidecarlson
  6

• problem running findtirs

  #42 opened 5 years ago by JennyHTLee
  5

• Install via singularity

  #40 opened 5 years ago by oushujun
  7

• Configure all external programs, even if they exist in PATH

  #41 opened 5 years ago by sestaton
  0

• Makefile.PL error

  #39 opened 5 years ago by dejonggr
  9

• output files explanation

  #33 opened 6 years ago by DiegoZavallo
  10

• Error Makefile.PL

  #37 opened 5 years ago by ohan-Bioinfo
  8

• ages file has different LTR names

  #35 opened 5 years ago by juancresc
  4

• Tephra docker run issue

  #27 opened 5 years ago by mb3188
  9

• LTR Age output

  #36 opened 5 years ago by DiegoZavallo
  8

• Can we run the command LTR age for our own files

  #34 opened 5 years ago by juancresc
  1

• Log does not appear to express long run times correctly

  #28 opened 5 years ago by sestaton
  1

• Illegal division by zero

  #32 opened 6 years ago by juancresc
  2

• Problems running

  #30 opened 6 years ago by juancresc
  3

• manual installation: missing modules for cpan in docs

  #31 opened 6 years ago by juancresc
  4

• How are options given at the CLI and configuration handled?

  #29 opened 6 years ago by sestaton
  0

• Expand install instructions

  #4 opened 6 years ago by sestaton
  2

• run failed

  #25 opened 6 years ago by ShowkyBioinformatics
  2

• 'maskref' command not cleaning up intermediate results

  #24 opened 6 years ago by sestaton
  1

• findnonltrs failed

  #22 opened 6 years ago by altingia
  4

• Refactor fragment search to not store files for each contig

  #23 opened 6 years ago by sestaton
  1

• error in creating LTR exemplar file

  #21 opened 7 years ago by sestaton
  1

• Need to make one exemplar output file and clean up from 'classifyltrs' command

  #19 opened 8 years ago by sestaton
  1

• coordinates are reversed for some helitrons, and do not match gff

  #20 opened 8 years ago by sestaton
  0

• IDs in GFF and FASTA do not match for findhelitrons command

  #18 opened 8 years ago by sestaton
  0

• sololtr command needs optimizing for large genomes

  #17 opened 8 years ago by sestaton
  0

• Output of 'illrecomb' command has formatting issues

  #16 opened 8 years ago by sestaton
  0

• Incorrect coordinates in LTR-RT GFF3

  #15 opened 8 years ago by sestaton
  1

• Need option to get age of all LTR elements

  #14 opened 8 years ago by sestaton
  0

• Consider alternatives for parsing GFF3

  #8 opened 8 years ago by sestaton
  1

• LTR-RT feature clustering needs optimizing

  #13 opened 8 years ago by sestaton
  1

• Add option to filter elements above a certain percent of N content

  #12 opened 8 years ago by sestaton
  0

• Add full working example

  #5 opened 8 years ago by sestaton
  0

• standardize FASTA identifiers for LTR commands

  #11 opened 8 years ago by sestaton
  0

• Try to configure emboss, samtools, hmmer3 automatically

  #10 opened 8 years ago by sestaton
  0

• Fix threading issue with ltrage command

  #7 opened 8 years ago by sestaton
  2

• classifyltrs command output shows high percentage of unclassified elements

  #9 opened 8 years ago by sestaton
  0

• Make configuration location an option

  #3 opened 8 years ago by sestaton
  0

• findnonltrs command will fail with system configuration

  #6 opened 8 years ago by sestaton
  1

• 'ltrage' command not working with multiple threads

  #2 opened 8 years ago by sestaton
  0