Only noncoding annotations returned despite protein-coding genes in reference DB

[schilau]

Hi, thanks for this tool!

I’m trying to use this tool, but I'm running into an issue where all annotations are classified as noncoding, even though my reference database clearly contains protein-coding genes.

Interestingly, this seems related to the already reported (but unresolved) issue:
#3

Instead of expected annotations like:

• CDS
• exon
• UTR

I only get:

• distnoncoding_intron500
• intergenic
• noncoding_exon
• proxnoncoding_intron500

---

I generated my own gffutils database from GENCODE:

• Source: GENCODE Comprehensive gene annotation
• Release: 49 (GRCh38.p14)

db = gffutils.create_db(
    annotation_file, dbfn=db_file, force=force,
    keep_order=True, merge_strategy='merge', sort_attribute_values=True,
    disable_infer_genes=False,
    disable_infer_transcripts=False
)

I verified that the database contains protein-coding genes: and got ~20,000 genes across ~290,000 transcripts.

---

Question:

Could this be related to how gene/transcript biotypes are parsed or expected by the annotator?

For example:

• Does the tool require specific attribute keys (e.g. gene_biotype vs gene_type)?
• Is there a compatibility issue with newer GENCODE releases?

Thanks a lot for your help!

[byee4]

Hi, it's possible it could be related to the open issue, but unless Gencode has recently changed their format, the annotations should have those gene types. Could you help me with a few lines of your unannotated file, so I can check? Is your data stranded?

[schilau]

Of course! I’m not able to upload a .bed file directly, so I simply changed the file extension.
Yes, my data is stranded!

Do you need any additional information? Thanks a lot!

test.bed.txt