prepareReference: Prepare reference data for the RNA-Seq Pipeline

In andrewtikhonov/ArrayExpressHTS: ArrayExpress High Throughput Sequencing Processing Pipeline

Description

prepareReference downloads reference genome or transcriptome for the selected organism from the Ensembl database and processes it so that it can be used by the pipeline. prepareReference requires an Internet connection.

Usage

    prepareReference(organism, version = "current", 
        type = c("genome", "transcriptome"), 
        location = getDefaultReferenceDir(), 
        aligner = c("bwa", "bowtie", "tophat"), 
        refresh = FALSE, run = TRUE)

Arguments

organism	supported organism names can be viewed in the Ensemble database. Check 'ftp://ftp.ensembl.org/pub'.
version	"current" or other appropriate version. Check 'ftp://ftp.ensembl.org/pub'.
type	two values are supported: "genome", "transcriptome"
location	indicates where the reference data should be stored.
aligner	3 types of aligners are supported: "bwa", "bowtie" and "tophat".
refresh	if TRUE, existing reference data will be rebuilt.
run	if FALSE, the downloading and processing commands will not be executed.

Value

The output is the version of the organism reference that has been downloaded and processed. The reference files are kept in the folder defined in location parameter.

Author(s)

Andrew Tikhonov <[e-mail]>, Angela Goncalves <[e-mail]>

See Also

ArrayExpressHTS, ArrayExpressHTSFastQ, prepareAnnotation

Examples

if (isRCloud()) {
        
    par(ask = FALSE)

    # the following piece of code will take ~3 hours to complete
    #
        
    # if executed on a local PC, make sure tools are available
    # to the pipeline.
    # 
        
    # create directory
    #
    # Please note, tempdir() is used for automamtic test 
    # execution. Select directory more appropriate and 
    # suitable for keeping reference data.
    #
    referencefolder = paste(tempdir(), "/reference", sep = "")
    
    dir.create(referencefolder)
    
    # download and prepare reference
    prepareReference("Homo_sapiens", version = "GRCh37.61", 
        type = "genome", aligner = "bowtie", location = referencefolder )
    prepareReference("Homo_sapiens", version = "GRCh37.61", 
        type = "transcriptome", aligner = "bowtie", location = referencefolder )
    prepareReference("Mus_musculus", version = "current", 
        type = "genome", aligner = "bowtie", location = referencefolder )
    prepareReference("Mus_musculus", version = "current", 
        type = "transcriptome", aligner = "bowtie", location = referencefolder )
}

andrewtikhonov/ArrayExpressHTS documentation built on May 28, 2019, 4:57 p.m.