available_genomes: Available Genomes

In Bishop-Laboratory/RLSeq: RLSeq: An analysis package for R-loop mapping data

Available Genomes

Description

Contains metadata about all the genomes available in UCSC. It contains derived metadata, such as the effective genome sizes as well. See also the data-raw/available_genomes.R script to see processing steps.

Usage

available_genomes

Format

An object of class data.frame with 199 rows and 27 columns.

Details

Structure

available_genomes is a data.frame with the following columns:

• UCSC_orgID

  • Official UCSC ID of the genome

• description

  • Verbose description of the assembly, source, and year/month of entry.

• nibPath

  • Endpoint of the genome in UCSC gbdb.

• organism

  • Name of the organism.

• defaultPos

  • Default location of genome browser view for this genome.

• active

  • Description not available.

• orderKey

  • Description not available.

• genome

  • The name of the genome.

• scientificName

  • The scientific name of the organism.

• htmlPath

  • Path in UCSC gbdb to the description.html file for the genome.

• hgNearOk

  • Description not available.

• hgPbOk

  • Description not available.

• sourceName

  • Name of organization providing the genome.

• taxId

  • The taxonomy ID of the organism.

• genes_available

  • If TRUE, the gene annotations are available in GTF format.

• year

  • The year the genome assembly was added.

• eff_genome_size_XXbp

  • The effective genome size of this genome. Calculated at various read lengths with khmer and used to improve the accuracy of analysis. See the data-raw/available_genomes.R script to see how this calculation was performed.

• genome_length

  • The total length of the genome.

• rlfs_available

  • If TRUE, R-loop forming sequences annotations are available in the RLBase AWS S3 repository.

Examples

available_genomes

Bishop-Laboratory/RLSeq documentation built on Jan. 28, 2023, 11:38 p.m.