Download UCSC reference genome

downloadUCSCGenome(organism, genomeBuild = NULL, outputDir = ".")

Arguments

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").

genomeBuild

character(1). Ensembl genome build assembly name (e.g. "GRCh38"). If set NULL, defaults to the most recent build available. Note: don't pass in UCSC build IDs (e.g. "hg38").

outputDir

character(1). Output directory path.

Value

Invisible list.

Note

Updated 2021-02-17.

Genome

  • <GENOME_BUILD>.chrom.sizes: Two-column tab-separated text file containing assembly sequence names and sizes.

  • <GENOME_BUILD>.chromAlias.txt: Sequence name alias file, one line for each sequence name. First column is sequence name followed by tab separated alias names.

Transcriptome

  • mrna.fa.gz: Human mRNA from GenBank. This sequence data is updated regularly via automatic GenBank updates.

  • refMrna.fa.gz: RefSeq mRNA from the same species as the genome. This sequence data is updated regularly via automatic GenBank updates.

Gene annotations

: This directory contains GTF files for the main gene transcript sets where available. They are sourced from the following gene model tables: ncbiRefSeq, refGene, ensGene, knownGene.

See also

Examples

## This example is bandwidth intensive. ## > downloadUCSCGenome(organism = "Homo sapiens")