UCSC hg38 FASTA File · Biostar

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UCSC hg38 FASTA File

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!

ucsc rnaseq hg38

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updated 4.2 years ago by Maximilian Haeussler

• written 4.2 years ago by BioC123 •

1 answer

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

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written 4.2 years ago by Pierre Lindenbaum

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/

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written 4.2 years ago by Maximilian Haeussler

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