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
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gmst same coords for begin and end for several start or stop codons #751
Having run etp mode on a genome with braker.pl version 3.0.3, occasionally gmst exon, CDS and start codons have the same coords for begin and end (field 4 equals field 5) or the exon, CDS and stop codon have the same field 4 and field 5 value. Is there a newer version that fixes this? Thanks for any insights.
--Jim Henderson
Here's a list of issues in this gff simply looking for same field 4 field 5 values
And here are data for one of these examples, g7266.t1 where 172710270 occurs twice in the CDS, exon and stop lines (all 5 gmst problems are similar with field 4 and 5 having same value at start or stop)
Having run etp mode on a genome with braker.pl version 3.0.3, occasionally gmst exon, CDS and start codons have the same coords for begin and end (field 4 equals field 5) or the exon, CDS and stop codon have the same field 4 and field 5 value. Is there a newer version that fixes this? Thanks for any insights.
--Jim Henderson
Here's a list of issues in this gff simply looking for same field 4 field 5 values
And here are data for one of these examples, g7266.t1 where 172710270 occurs twice in the CDS, exon and stop lines (all 5 gmst problems are similar with field 4 and 5 having same value at start or stop)