get_phix_genome: Download genome (fasta), annotation (GTF) and contaminants
In JokingHero/ORFik: Open Reading Frames in Genomics

get_phix_genome

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. By default, it will use ensembl reference, upon completion, the function will store a file called file.path(output.dir, "outputs.rds") with the output paths of your completed genome/annotation downloads. For most non-model nonvertebrate organisms, you need my fork of biomartr for it to work: remotes::install_github("Roleren/biomartr) 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 Illumina control reads. ORFik defines Phix as a contaminant genome. Phix is used in Illumina sequencers for sequencing quality control. Genome is: refseq, Escherichia phage phiX174. If sequencing facility created fastq files with the command `bcl2fastq`, then there should be very few phix reads left in the fastq files recieved.
`output.dir`	directory to save downloaded data
`gunzip`	logical, default TRUE, uncompress downloaded files that are zipped when downloaded, should be TRUE!

Details

Some files that are made after download:
- A fasta index for the genome
- A TxDb to speed up GTF/GFF reading
- Seperat of merged contaminant files
Files that can be made:
- Gene symbols (hgnc, etc)
- Uniprot ids (For name of protein structures)
If you want custom genome or gtf from you hard drive, assign existing paths like this:
annotation <- getGenomeAndAnnotation(GTF = "path/to/gtf.gtf", genome = "path/to/genome.fasta")

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.

References

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919035/

Examples


## Get Saccharomyces cerevisiae genome and gtf (create txdb for R)
#getGenomeAndAnnotation("Saccharomyces cerevisiae", tempdir(), assembly_type = "toplevel")
## Download and add pseudo 5' UTRs
#getGenomeAndAnnotation("Saccharomyces cerevisiae", tempdir(), assembly_type = "toplevel",
#  pseudo_5UTRS_if_needed = 100)
## 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)

# Drosophila melanogaster (toplevel exists only)
#getGenomeAndAnnotation("drosophila melanogaster", output.dir = file.path(config["ref"],
# "Drosophila_melanogaster_BDGP6"), assembly_type = "toplevel")
## 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):
# fixed_gff <- fix_malformed_gff("~/Desktop/test_plant/Arabidopsis_thaliana_genomic_refseq.gff")
## Then updated arguments:
# annotation <- c(fixed_gff, "~/Desktop/test_plant/Arabidopsis_thaliana_genomic_refseq.fna")
# names(annotation) <- c("gtf", "genome")
# Then make the txdb (for faster R use)
# makeTxdbFromGenome(annotation["gtf"], annotation["genome"], organism = "Arabidopsis thaliana")

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.