Problems with attributes in featureCounts -- GFF3 input instead of GTF

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I’m trying to run featureCounts for zebrafish, however it returns the error:

ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
The specified gene identifier attribute is ‘gene_id’
An example of attributes included in your GTF annotation is’ ID = id1; Parent = rna0; Dbxref = GeneID: 192301, Genbank: NM_173235.3, ZFIN: ZDB-GENE-020419-25; gbkey = mRNA; gene = rpl24; product = ribosomal protein L24; transcript_id = NM_173235.3 ’

Something similar occurs when running htseq-count.
Does anyone know how to solve?

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Welcome @petenbender

Your annotation appears to be in GFF3 format, not GTF. There is no gene_id attribute in the 9th column of GFF3 data.

Both Featurecounts and HTseq-count expect GTF input, as explains on the tool forms and as reported in errors.

Please review the FAQs below if you are not sure about the datatype difference. The tags added to your post also point to similar help from prior Q&A.

Thanks!

Thanks!

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Did you ever resolve this issue? I am having almost the exact same problem running featurecounts with a gff3 from maize

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Resolved in here: Featurecounts error using a gene annotation from a gff3 file