Is Whole Genome Fasta same for ensemble and knowgene annotation?
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.
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donny.dw •
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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.