Hello All,

Curious to know if anyone has experience merging transcriptome-derived gene models (e.g. Transdecoder predicted gene models) with BRAKER derived gene models to generate the final final gene model sets?.

Example of two format that needed to be merged; ...

File A from TransDecoder:
Scaffold_1  transdecoder    gene    4131480 4134369 .   +   .   ID=STRG.10;Name=ORF%20type%3Acomplete%20len%3A285%20%28
Scaffold_1  transdecoder    mRNA    4131480 4134369 .   +   .   ID=STRG.10.1.p1;Parent=STRG.10;Name=ORF%20type%3A
Scaffold_1  transdecoder    five_prime_UTR  4131480 4132453 .   +   .   ID=STRG.10.1.p1.utr5p1;Parent=STRG.10.1.p1
Scaffold_1  transdecoder    exon    4131480 4134369 .   +   .   ID=STRG.10.1.p1.exon1;Parent=STRG.10.1.p1
Scaffold_1  transdecoder    CDS 4132454 4133308 .   +   0   ID=cds.STRG.10.1.p1;Parent=STRG.10.1.p1
Scaffold_1  transdecoder    three_prime_UTR 4133309 4134369 .   +   .   ID=STRG.10.1.p1.utr3p1;Parent=STRG.10.1.p1

File B from BRAKER:
Scaffold_1  AUGUSTUS    transcript  415871  417382  0.37    -   .   anno2.g32044.t1
Scaffold_1  AUGUSTUS    stop_codon  415871  415873  .   -   0   transcript_id "anno2.g32044.t1"; gene_id "g_429296";
Scaffold_1  AUGUSTUS    CDS 415871  417382  0.37    -   0   transcript_id "anno2.g32044.t1"; gene_id "g_429296";
Scaffold_1  AUGUSTUS    exon    415871  417382  .   -   .   transcript_id "anno2.g32044.t1"; gene_id "g_429296";
Scaffold_1  AUGUSTUS    start_codon 417380  417382  .   -   0   transcript_id "anno2.g32044.t1"; gene_id "g_429296";

...

Regards, B