I have a difficulty to choose the suitable source for me. There are 3 ways that I consider to use the reference genome. I'm really confused.
- From HISAT2 website. "tran" version (contains GTF) as @Carlo Yague mentioned in my previous post. [It is not updated, last version from March 2016, I prefer to use the updated one.]
- From GENCODE website. as @krushnach80 mentioned in my previous post. Release 28 (GRCh38.p12), GTF file at the first section
gencode.v28.annotation.gtf, FASTA file which contains all chromosomes (Genome sequence (GRCh38.p12):
- From Ensembl website. GTF and FASTA files from this link. GTF: release 93, FASTA: downloading all chromosomes separately (One of my friends use this way for the reference genome of mouse) or downloading toplevel one (My another friend was unable to index this one.)
How should I evaluate these options? HISAT2 option seems the most comfortable one, but I don't want to use outdated one.