Questions regarding tsebra

[bauerlev]

Hello, I have a few questions regarding tsebra. I know it has it's own github, but it doesn't seem to be active and your group is the same maker so I'm hoping this is an appropriate place to ask.

1. What do each of these parameters in the config file actually mean? I can't find an answer in the documentation anywhere.

Allowed difference for each feature

Values have to be in [0,2]

e_1 0.0 e_2 0.5 e_3 0.096 e_4 0.02 e_5 0.18 e_6 0.18

2. Is there documentation on how the script get_longest_isoform works? We noticed multiple transcripts for a given loci after attempting to run braker3, so I tried this script and while it helped there are still instances where there's more than one transcript for a given locus.

Thanks for your help! We've been having significantly better success with braker over maker and I'm very grateful.