No start_codon and stop_codon in GTF file

[Tang-pro]

Hi @andrewprzh

isoquant.py --reference Genome.fa --complete_genedb --genedb genome.gtf --bam Y2_5_1.bam Y2_5_2.bam Y2_10_1.bam Y2_10_2.bam Y2_15_1.bam Y2_15_2.bam --label Y2_5_1 Y2_5_2 Y2_10_1 Y2_10_2 Y2_15_1 Y2_15_2 --data_type nanopore --prefix Y2quant --threads 40 --output Isoquant/Y2 --sqanti_output

After running the above command, why do I get a GTF file with no start_codon and stop_codon information in it?

[andrewprzh]

Hi @Tang-pro

Does you initial GTF annotation contain start and stop codons?
IsoQuant by itself only detects genes, transcripts and exons.

Best
Andrey

[Tang-pro]

@andrewprzh
okay, thanks.
My initial GTF annotation doesn't include start and stop codons. What methods or software can I use to calculate them?

[andrewprzh]

@Tang-pro

Unfortunately, I don't have any experience with that. Probably you need some kind of gene prediction software, maybe something like https://github.com/ConesaLab/IsoAnnot

Best
Andrey