UCSC hg38 FASTA File

Question

[BioC123]

Hi

I'm doing an RNA Seq experiment and I'm trying to align the reads using Rsubread package in R. I need to have UCSC hg38 FASTA file for building the index. Is there are place to download the file?

Thank you!

Answer 1

[Pierre Lindenbaum]

hg38.fa.gz under https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

[Maximilian Haeussler]

If you read that page, you find that UCSC points to the "analysisSet" because it doesn't contains haps/alts/fixes and that directory points to NCBI, because they have already precalculated indices: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/