Hello I made my own gtf file from hmmer results and I used it to calculate abundance of genes from the annotated feature of my gtf file using featureCounts program. The error message that I got is the following:
featureCounts -p -O -T 9 -F gtf -t gene -a demo.gff -o demo_fcounts.txt demo_sorted.bam
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 'gene_id "4_hydroxyacetophenone";E-value "3.5e-192";Score "649.8";Target "k141_179264"'
I have read similar issues published but seems like they do not resolve my problem.
This is the structure of my gtf table:
|4_hydroxyacetophenone||hmmsearch||gene||3558||5087||2.6e-180||-||.||gene_id "4_hydroxyacetophenone";E-value "2.6e-180";Score "610.5";Target "k141_165782"|
|4_hydroxyacetophenone||hmmsearch||gene||151||1617||3.5e-192||+||.||gene_id "4_hydroxyacetophenone";E-value "3.5e-192";Score "649.8";Target "k141_179264"|
for my knowledge featureCounts must look at the attributes table and match the feature coordinates (in my case the gene feature type coordinates) with the contig ID (e.g. in the first row: K_141_165782) and it seems to not recognize the gene ID. Is it letting some other attribute ? or instead of providing the gene in the seqid column I should provide the contig ID K_141_165782 (first row example) ?
Thanks for your time.