get_noncoding_rna {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_noncoding_rna(ncRNA, output.dir, organism, gunzip)
ncRNA |
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
gtf. |
output.dir |
directory to save downloaded data |
organism |
scientific name of organism, Homo sapiens,
Danio rerio, Mus musculus, etc. See |
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()
## Get Saccharomyces cerevisiae genome and gtf (create txdb for R) #getGenomeAndAnnotation("Saccharomyces cerevisiae", tempdir(), assembly_type = "toplevel") ## Get Danio rerio genome and gtf (create txdb for R) #getGenomeAndAnnotation("Danio rerio", tempdir()) output.dir <- "/Bio_data/references/zebrafish" ## Get Danio rerio and Phix contamints to deplete during alignment #getGenomeAndAnnotation("Danio rerio", output.dir, phix = TRUE) ## Optimize for ORFik (speed up for large annotations like human or zebrafish) #getGenomeAndAnnotation("Danio rerio", tempdir(), optimize = TRUE) ## How to save malformed refseq gffs: ## First run function and let it crash: #annotation <- getGenomeAndAnnotation(organism = "Arabidopsis thaliana", output.dir = "~/Desktop/test_plant/", # assembly_type = "primary_assembly", db = "refseq") ## Then apply a fix (example for linux, too long rows): # \code{system("cat ~/Desktop/test_plant/Arabidopsis_thaliana_genomic_refseq.gff | awk '{ if (length($0) < 32768) print }' > ~/Desktop/test_plant/Arabidopsis_thaliana_genomic_refseq_trimmed2.gff")} ## Then updated arguments: annotation <- c("~/Desktop/test_plant/Arabidopsis_thaliana_genomic_refseq_trimmed.gff", "~/Desktop/test_plant/Arabidopsis_thaliana_genomic_refseq.fna") names(annotation) <- c("gtf", "genome") # Make the txdb (for faster R use) # makeTxdbFromGenome(annotation["gtf"], annotation["genome"], organism = "Arabidopsis thaliana")