Is the gene_id attribute in the GTF files analogous to the Name attribute in the .gff3 file? Because both featureCounts and htseq-count have the default id attribute as gene_id but I have .gff3 so I'm trying to figure out what I should change it to? Thanks.
Correct me if I'm wrong but it may not be straightforward to apply htseq-count to gff3 (I don't know about featureCount). For typical differential gene expression, htseq-count needs an attribute that groups all the exons belonging to the same gene, the gene_id is usually the right one for gtf. But I don't think gff3 necessarily has such attribute.
See also How to modify a gff3 file for HTSeq?