search

Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
Other
364 stars 81 forks source link

braker.gff3 and braker.gtf #700

Closed woodoo46 closed 1 year ago

woodoo46 commented 1 year ago

Hi there,

When we run the pipeline with --gff3 is specified, the number of lines in file braker.giff3 and braker.gtf are supposed to be the same? In my case, the number of lines do not match

1689657 braker.gff3 1738870 braker.gtf

For example, in the gff3 file, we are missing this line in gtf file.

tig000001 GeneMark.hmm3 transcript 22093 23471 . + . g1.t2

I checked the files, the difference coming from lines whose feature is "mRNA" or "transcript". So I guess this is not very important?

Thanks!

George

LarsGab commented 1 year ago

Hi,

the number of lines between the formats might differ slightly. Despite this, the content of the files is the same. Note that we fixed some issues with the gff3 format, so please make sure that you are using the latest version of BRAKER.

Best, Lars