9th column of the GTF file is exon_id instead of gene_id, is this normal?

Question

[Kai_Qi]

Hi:

For RNA-seq analysis, the GTF I have used was downloaded from here : I used the genes.gtf for indexing the genome. But today, when I use featureCount I found that in this GTF the 9th column is exon_id:

$ head genes.gtf 
1   processed_transcript    exon    11869   12227   .   +   .   exon_id "ENSE00002234944"; exon_number "1"; gene_biotype "pseudogene"; gene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "ensembl_havana"; transcript_id "ENST00000456328"; transcript_name "DDX11L1-002"; transcript_source "havana"; tss_id "TSS15133";
1   processed_transcript    transcript  11869   14409   .   +   .   gene_biotype "pseudogene"; gene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "ensembl_havana"; transcript_id "ENST00000456328"; transcript_name "DDX11L1-002"; transcript_source "havana"; tss_id "TSS15133";

After reading a while it occurred to me that under most of cases the 9th column of a GTF file should be a gene_id. Does this mean that all the work I have doing by using this indexed genome for analysis could be inappropriate? If not, what should I feed the GTF.attrType for featurecounts?

Thank you very much,

[Ram]

The 9th column of a GTF file is a ; separated list of key value pairs, where the key and the value are space-separated. There is no general "gene_id" as 9th column convention as such - only that the 9th column can and generally does contain a gene_id if the feature is of type gene or transcript. Since the feature type is exon here, I am not surprised seeing an exon_id.

[Kai_Qi]

So does this mean there is no problem using this GTF for indexing and downstream analysis (differential gene expression)? I feel if the parameter of my featureCounts is:

featureCount(files, annot.ext="genes.gtf", isGTFannotationFile=TRUE, GTF.featureType="exon", GTF.attType="exon_id",...)

I would probably get the count of exons.

If I wanted to get the count of genes maybe I should use:

`featureCount(files, annot.ext="genes.gtf", isGTFannotationFile=TRUE, GTF.featureType="exon", GTF.attType="gene_id",...)`

instead? Sorry for being naive. I feel just began to be familiar with the general process.