TSEBRA

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Hello, I am trying to combine two runs of BRAKER3: one using short reads and protein data, the other using long-reads and protein data (using the braker_lr branch). Would the...

danielwood1992

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

1

I execute the script with a single ```braker.gtf``` file and the error still persists in the updated version (I've gone through the issue mentioned at #34 ). ``` get_longest_isoform.py --gtf...

sahoo-rk

Still need to remove redundant sequences after gtf files recombination?

1

Hi, I used TSEBRA and successfully obtained the combined tsebra.gtf integrates the short-read, protein and long-read gtf files generated by braker, do I need another redundant sequence filtration with tools...

Flyase

Hi there I am a bit confused about how the default parameters in the default.cfg file are described (and chosen): ``` # Weight for each hint source # Values have...

sjannielefevre

The TSEBRA result to UCSC or Ensemble type

1

Dear developer: We are wondering if there is any way to convert BREAKER and TSEBRA results into comment files for NCBI or Ensemble commits? If we have this function, I...

ld9866

Hi, I tried running tsebra using the *long_reads* branch but I'm getting this error. ``` ### BUILD OVERLAP GRAPH Traceback (most recent call last): File "/home/guibo205/git/TSEBRA/bin/tsebra.py", line 224, in main()...

gbdias

Combining TSEBRA Output with other Annotations in GFF format

1

Hello, I am trying to wrap my head around how best to merge these annotations. We have information from EMapper and Interproscan we would like to merge with he TSEBRA...

NicMAlexandre

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

1

Hi, I was running TSEBRA with both the default.cfg and keep_ab_initio.cfg. The first run with the default.cfg was successful, however, the run the keep_ab_initio.cfg failed with the following error: ```...

Huiting120

Hello! I have used braker for gene prediction with protein of close homology and RNAseq data together (Trial 1) and I ran braker separately with protein of close homology and...

ShakunthalaNatarajan

How to improve the BUSCO score of the resulted predictions?

6

Dear Lars, Thanks for your valuable advice. I have tried the latest version of TSEBRA and BRAKER. The BUSCO score have improved a lot but I still have some questions....

bioinformaticspcj