Question: Differences between ensembl gtf files and gff3 file
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gravatar for oma219
3.8 years ago by
oma21930
oma21930 wrote:

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.

sequencing • 1.7k views
ADD COMMENTlink modified 3.8 years ago by dariober11k • written 3.8 years ago by oma21930
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GTF Format reference from Ensembl. GFF3 format reference from GMOD.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by GenoMax96k
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gravatar for dariober
3.8 years ago by
dariober11k
WCIP | Glasgow | UK
dariober11k wrote:

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?

ADD COMMENTlink written 3.8 years ago by dariober11k
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