Marcel Schilling

I suspect the problematic entries come from [this GFF file](https://github.com/guigolab/gencode-cls-master-table/releases/download/EnhancedAnnotationv3.0/Hv3_enhancedCLS3_refined_+gencodev43.loci.refmerged.gff.gz) which defines some pairs of genes with the exact same coordinates and structure but different IDs.

I need the merged annotation in both, GTF and GFF format (for different downstream tools). Currently I am running `agat_sp_merge_annotations.pl` with a config that contains ```yaml output_format: GFF gff_output_version: 3...

I am not sure which FASTA file you refer to. I have two annotations, the GFF one I linked above and one GTF I am not at liberty to share...

@Juke34: Is there anything I can do to troubleshoot this further or do I need to give up on using AGAT and find an alternative approach to generate my GTF?...

@Juke34: I am not sure what else I need to provide for you fix this. AFAICT, [the GFF I already linked above](https://github.com/guigolab/gencode-cls-master-table/releases/download/EnhancedAnnotationv3.0/Hv3_enhancedCLS3_refined_+gencodev43.loci.refmerged.gff.gz) is causing the quoted attributes cellranger complains about.

Thank you. Will test and let you know. Else I'll track down the FASTA and share a public link.

I am still seing some multi-value tags (incl. `tag`, `gene_name`, & `transcript_name`) with this version (I *do* get a lot of the 'keeping only the first one' messages though). ---...

@Juke34: > Does it work with cellranger? No. It seems to be throwing off there parser. A line with double `tag` value triggers an error about unexpected quotes in `gene_name`,...

@Juke34 > Yes I remove double attributes only for gene_id and transcript_id as it is the only sensible attributes to get a consistent file. Also, would it be possible to...

Now that I have a better understanding how to identify these cases I can trace them back more easily and potentially provide you with a more minimal breaking input.