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_noncoding_rna(ncRNA, output.dir, organism, gunzip)
logical or character, default FALSE (not used, no download),
ncRNA is used as a contaminant genome.
If TRUE, will try to find ncRNA sequences from the gtf file, usually represented as
lncRNA (long noncoding RNA's). Will let you know if no ncRNA sequences were found in
directory to save downloaded data
scientific name of organism, Homo sapiens,
Danio rerio, Mus musculus, etc. See
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.
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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)
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