Entering edit mode
21 months ago
BioinfoBee
•
0
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
