Is Whole Genome Fasta same for ensemble and knowgene annotation?

Question

[donny.dw]

I am using STAR to generate genome reference.

I need use ensemble gtf file, hg38.ensGene.gtf.

I found WholeGenomeFasta on iGenomes and UCSC. They are not for ensemble. They are in UCSC/hg38 folder.

Is there a specific WholeGenomeFasta for ensembl annotation? Can I use hg38.ensGene.gtf and UCSC hg38 whole genome fasta to generate genome reference.

[Asaf]

You might get some insights from Heng Li's blog: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use (or get more confused, though). EnsEMBL genes should be same as gencode genes but these should have chromosome names that match UCSC/RefSeq.