in the tsebra combined annotation, why does same position have different gene ids?

[joleneyue]

Dear developer,

i did the following and found the problem in the tsebra combined annotation : same position(same gene model) has different gene ids.

1: #fix the gene ids before running tsebra:

   ./bin/fix_gtf_ids.py --gtf braker1_out/braker.gtf --out braker1_fixed.gtf
   ./bin/fix_gtf_ids.py --gtf braker2_out/braker.gtf --out braker2_fixed.gtf

2. #run tsebra for the fixed gtf files:

   ./TSEBRA/bin/tsebra.py -g braker1/braker1_fixed.gtf, braker2/braker2_fixed.gtf -c TSEBRA/config/default.cfg -e 
    braker1/hintsfile.gff,braker2/hintsfile.gff -o braker1+2_combined_fixed.gtf
   

my configure file look like this :

config file:

  # src weights
  P 0.1
  E 10
  C 5
  M 1
  # Low evidence support
  intron_support 0.2
  stasto_support 1
  # Feature differences
  e_1 0
  e_2 0.5
  e_3 25
  e_4 10

i uploaded the combined braker gtf file onto Coge and i found in the location: "HiC_scaffold_3:51967376..51972825" , there is one gene model but it has two different gene ids : anno2.g5617.t1 and anno1.g6823.t1.

i do not know why this problem occur and how to solve it.

Can you let me know? Thanks a lot.
Cheers,
Yuling

[LarsGab]

Hi,
this repository was only active during early development. Please use the TSEBRA version from here.

Best,
Lars