Gaius-Augustus/TSEBRA

Issues

• Does get_longest_isoform.py keep ab initio predictions?

  #52 opened 3 months ago by tinameiring
  1

• Selecting protein sequences after merging annotation sets; what do the anno1 and anno2 prefixes mean in gtf file?

  #21 opened a year ago by robertwhbaldwin
  1

• Combine BRAKER3 and Galba annotation for new, non-model genome

  #51 opened 6 months ago by YanisChrys
  0

• Combining runs of BRAKER3 with short and long-read RNA-seq

  #50 opened 7 months ago by danielwood1992
  0

• Execution issue still persists with ```get_longest_isoform.py```

  #49 opened 9 months ago by sahoo-rk
  1

• Still need to remove redundant sequences after gtf files recombination?

  #46 opened 10 months ago by Flyase
  1

• An error occurred while running 'get_longest_isoform.py'

  #34 opened a year ago by MICHELLE-LMX
  3

• Confusion about the default config parameters

  #45 opened a year ago by sjannielefevre
  0

• The TSEBRA result to UCSC or Ensemble type

  #39 opened a year ago by ld9866
  1

• `--ignore_tx_phase` on branch long_reads

  #38 opened a year ago by gbdias
  2

• Transcripts assigned separate gene IDs after combining GTFs

  #32 opened a year ago by GwynHN
  3

• genomethreader

  #31 opened a year ago by bijendrabio
  2

• where is the gff2aa.pl script?

  #30 opened a year ago by joleneyue
  2

• New default.cfg increased duplicated BUSCO

  #29 opened a year ago by Huiting120
  1

• Tsebra gtf2aa.pl predicting proteins with in-frame stop codons

  #24 opened a year ago by nllg
  1

• BUSCO completeness decrease after tsebra

  #23 opened a year ago by yimingweng
  2

• How to convert gtf file from TSEBRA to gff3 file as EVM input？

  #22 opened a year ago by yweii
  4

• How to get a full merge of protein-based and RNA-seq-based predictions without rejecting any?

  #20 opened a year ago by SchwarzEM
  2

• TSEBRA for merging several evidences

  #18 opened a year ago by marco91sol
  1

• The Genemark and Augustus profile from TSEBRA

  #5 opened a year ago by wyim-pgl
  2

• long_reads branch issue

  #36 opened a year ago by gbdias
  0

• Combining TSEBRA Output with other Annotations in GFF format

  #35 opened a year ago by NicMAlexandre
  1

• Contained Gene bug

  #26 opened 2 years ago by nhartwic
  3

• Complementing curated genes with TSEBRA + other concerns

  #13 opened 2 years ago by nicmoya
  12

• TSEBRA failed with keep_ab_initio.cfg (but worked with default.cfg)

  #28 opened 2 years ago by Huiting120
  1

• Number of genes predicted with TSEBRA is more while BUSCO score remains the same

  #25 opened 2 years ago by ShakunthalaNatarajan
  0

• benchmarking TSEBRA with BUSCO: my results are not good

  #6 opened 3 years ago by amvarani
  7

• How to improve the BUSCO score of the resulted predictions?

  #19 opened 2 years ago by bioinformaticspcj
  6

• Gene model encompasses multiple unique genes without overlapping transcripts

  #15 opened 2 years ago by ckeeling
  4

• braker2 - proteins

  #12 opened 2 years ago by minhasbushra
  2

• Inconsistencies in transcript_ID and gene_ID

  #14 opened 2 years ago by minhasbushra
  2

• Non-overlapping isoforms

  #16 opened 2 years ago by alexcorm
  3

• How can we translate our TSEBRA result gtf to NCBI gtf

  #17 opened 2 years ago by ld9866
  3

• How to get aa and CDS sequences

  #7 opened 3 years ago by SC-Duan
  7

• detailed document for the configure setting

  #8 opened 3 years ago by sotuamax
  5

• tsebra says skipping transcripts with missing CDS and exons, but which have both in the input gtf files

  #2 opened 3 years ago by adamfreedman
  17

• evidence.AttributeMissing: Source of Hint is missing

  #11 opened 3 years ago by yplee614
  0

• how can I add braker-generated UTR features into TSEBRA out ?

  #10 opened 3 years ago by tinyfallen
  11

• conflicting parents with gtf2gff.pl

  #9 opened 3 years ago by conchoecia
  2

• TSEBRA generates gtf file without 'gene' meta-feature in the third column

  #4 opened 3 years ago by dieunelderilus
  1

• Naming is incorrect

  #3 opened 3 years ago by sarjopp
  1

• licence file missing

  #1 opened 4 years ago by MarioStanke
  0