get_phix_genome {ORFik} | R Documentation |
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.
get_phix_genome(phix, output.dir, gunzip)
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! |
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"
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.
Other STAR:
STAR.align.folder()
,
STAR.align.single()
,
STAR.allsteps.multiQC()
,
STAR.index()
,
STAR.install()
,
STAR.multiQC()
,
STAR.remove.crashed.genome()
,
install.fastp()
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)