GTF/GFF3 file compatible with (GRCh38/hg38)(hg38)

Question

[kanwarjag]

I am using Reference genome -Human Dec2013 (GRCh38/hg38)(hg38) and gene model Homo_sapiens.GRCh38.101.gff3.gz however I get error saying chromosome naming is not matching. I know that Ensembel uses Chr as prefix. The question is if I use Human Dec2013 (GRCh38/hg38)(hg38) as reference assembly, which gene model file of hg38 should be compatible without editing gene model gtf or gff3 file and from where I can download? Will Gencode GRCh38 GTF file be compatible with Human Dec2013 (GRCh38/hg38)(hg38)? Thanks

[AISHA]

Is the reference genome from NCBI..? If yes, NCBI also provides gff.

[colindaven]

I would download everything again from the same source and learn to always check chr names in a text editor before using.

I recommend ENSEMBL and GenCode for good, consistent resources. I have had better experiences there than with NCBI or UCSC efforts.