Oshlack/Lace

Issues

• Python version should be downgraded in environment.yml

  #55 opened 2 years ago by asan-emirsaleh
  3

• 'DiGraph' object issue on networkx 2.3

  #56 opened 2 years ago by asan-emirsaleh
  1

• Lace processed without any files being produced.

  #57 opened 2 years ago by asan-emirsaleh
  2

• (installation) In environment.yml, fix Python Version

  #54 opened 4 years ago by lmuenter
  1

• Assessing completeness of SuperTranscript transcriptome assembly/BUSCO

  #53 opened 4 years ago by MariaBuenner
  3

• failed install Lace

  #51 opened 4 years ago by Lix1993
  4

• Failed to construct

  #46 opened 6 years ago by cd-ccmb
  1

• Please add shebangs to the python scripts

  #48 opened 5 years ago by dpryan79
  1

• -1 Transcripts and Whirls for some gene entries

  #45 opened 5 years ago by sarahhp
  2

• Does a cluster mean a unigene or transcript?

  #47 opened 5 years ago by wang-tianpeng
  1

• Wrong example name

  #50 opened 5 years ago by smoretti
  1

• Raise error when networkx version is too high

  #43 opened 6 years ago by sarahhp
  4

• Excessive memory usage on large dataset

  #42 opened 6 years ago by sarahhp
  5

• mv: cannot stat ....

  #40 opened 6 years ago by nadiadavidson
  1

• Question: supertranscripts (conceptual question)

  #36 opened 6 years ago by sofiapar265
  1

• Problem with memory exceeding the limit.

  #29 opened 6 years ago by nadiadavidson
  4

• Question: use SuperTranscripts for paralogs

  #33 opened 6 years ago by hydrahamster
  1

• SuperDuper.gff not consistent with gff2 standard

  #30 opened 6 years ago by nadiadavidson
  0

• Ask for help about this condition。

  #38 opened 6 years ago by zyworship
  1

• Lace stalls without error ...

  #31 opened 6 years ago by dietmarpils
  2

• DTE and DTU without biological replicates ?

  #39 opened 6 years ago by med1104
  1

• analysing blat is failing

  #34 opened 7 years ago by Dramenia
  9

• Logging

  #11 opened 8 years ago by Quarkins
  0

• Have ribbon write intermediate fasta and psl file to a subdirectory

  #15 opened 8 years ago by nadiadavidson
  0

• Not reverse complimenting the strand when it should

  #20 opened 8 years ago by nadiadavidson
  1

• In the help info, I think we should use the word "TranscriptFile" instead of "GenomeFile"

  #19 opened 8 years ago by nadiadavidson
  1

• Speed

  #12 opened 9 years ago by Quarkins
  1

• Issues from Lukes review

  #13 opened 9 years ago by Quarkins
  1

• Addtional functionality

  #6 opened 9 years ago by Quarkins
  2

• Add flag to contig IDs when the topo sorting hasn't gone to plan

  #8 opened 9 years ago by nadiadavidson
  1

• Remove ".fasta" from contig IDs in SuperDuper.fasta

  #7 opened 9 years ago by nadiadavidson
  1

• End coordinate off by one in gff

  #9 opened 9 years ago by nadiadavidson
  1

• SuperDuperTrans.gff has wrong entries for special cases

  #10 opened 9 years ago by nadiadavidson
  1

• Bed or gff format output

  #2 opened 9 years ago by nadiadavidson
  1

• Dealing with reverse compliments

  #3 opened 9 years ago by nadiadavidson
  1

• gff table needs another column

  #5 opened 9 years ago by nadiadavidson
  1

• ParaCluster.py can't work with a single gene as input

  #4 opened 9 years ago by nadiadavidson
  1

• Test

  #1 opened 9 years ago by nadiadavidson
  0