jolbi
commented
11 months ago Hi,
First thank you for this amazing tool!
I am facing similar problem. My gff includes mRNA, CDS, exon, five-prime-UTR and three-prime-UTR, but no gene. In my case, mRNA feature includes parent (gene) ID, but there are no gene feature rows in gff.
If I use -infer_genes flag without providing mRNA as feature type (-f ) I get the same error. If I use -f flag, the error is gone but no gene features are added to gff.
Which feature names does this function use to infer parent feature?
The workaround for my case was using AGAT's agat_convert_sp_gxf2gxf.pl on output gff to automatically add gene features. Hope this helps someone.
Hi,
Your software seems perfect for generating an annotation file I need for a manuscript I'm working on. However, I'm having an issue with it:
I have a gtf file with the following features, CDS, exon, start_codon, stop_codon.
I used the flags -infer_genes -infer_transcripts since I don't have those features, but then when I run Liftoff, it gives me the error, "GFF does not contain any gene features. Use -f to provide a list of other feature types to lift over."
But based on your documentation, it seems like using -infer_genes and -infer_transcripts is meant for exactly the case I have in my gtf file. Is this a bug, or am I doing something incorrectly with it? Thanks!