map gene ids back to gff

[mili-ai]

Thank you so much for your tool! I have genome files and annotation GFF files for two species, and I mainly want to use TOGA to identify orthologs between them. However, when I run it, the gene IDs and transcript IDs for the query species in the orthology_classification.tsv file don't match the gene and transcript IDs in my original annotation file. Could you suggest how to map the gene and transcript IDs back to my original annotation file? Should I do this based on the positions in the query_annotation.bed file, or is there a better way to do this?

[MichaelHiller]

Hi,
we provide bed and gtf format. For gtf, we use UCSC's genePredToGtf to convert bed to gtf.
This tool is know to have issues with assigning the gene name properly.

Alejandro wrote a new converter
https://github.com/alejandrogzi/bed2gtf
https://github.com/alejandrogzi/bed2gff

Pls try this tool, hoping that this will fix these issues