available_genomes {RLSeq} | R Documentation

## 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

[Package RLSeq version 1.0.0 Index]