get_phix_genome {ORFik} | R Documentation

## Download genome (fasta), annotation (GTF) and contaminants

### Description

This function automatically downloads (if files not already exists) genomes and contaminants specified for genome alignment. Will create a R transcript database (TxDb object) from the annotation.
It will also index the genome for you
If you misspelled something or crashed, delete wrong files and run again.
Do remake = TRUE, to do it all over again.

### Usage

    get_phix_genome(phix, output.dir, gunzip)

### Arguments

`phix` | logical, default FALSE, download phix sequence to filter out with. Phix is used as a contaminant genome. Only use if illumina sequencing. Phix is used in Illumina sequencers for sequencing quality control. Genome is: refseq, Escherichia virus phiX174
`output.dir` | directory to save downloaded data
`gunzip` | logical, default TRUE, uncompress downloaded files that are zipped when downloaded, should be TRUE!

### Details

If you want custom genome or gtf from you hard drive, assign it after you run this function, like this:
annotation <- getGenomeAndAnnotation(GTF = FALSE, genome = FALSE)
annotation["genome"] = "path/to/genome.fasta"
annotation["gtf"] = "path/to/gtf.gtf"

### Value

a named character vector of path to genomes and gtf downloaded, and additional contaminants if used. If merge_contaminants is TRUE, will not give individual fasta files to contaminants, but only the merged one.

### See Also

Other STAR: `STAR.align.folder()`, `STAR.align.single()`, `STAR.allsteps.multiQC()`, `STAR.index()`, `STAR.install()`, `STAR.multiQC()`, `STAR.remove.crashed.genome()`, `install.fastp()`

### Examples

    output.dir <- "/Bio_data/references/zebrafish"
    #getGenomeAndAnnotation("Danio rerio", output.dir)

    ## Get Phix contamints to deplete during alignment
    #getGenomeAndAnnotation("Danio rerio", output.dir, phix = TRUE)

[Package ORFik version 1.10.13 Index]