download.ebi: Faster download of fastq files

In ORFik: Open Reading Frames in Genomics

Description

Uses ftp download from vol1 drive on EBI ftp server, for faster download of ERR, SRR or DRR files. But does not support subsetting or custom settings of files!

Usage

download.ebi(info, outdir, rename = TRUE, BPPARAM = bpparam())

Arguments

info	character vector of only SRR numbers or a data.frame with SRA metadata information including the SRR numbers in a column called "Run" or "SRR". Can be SRR, ERR or DRR numbers. If only SRR numbers can not rename, since no additional information is given.
outdir	a string, default: cbu server
rename	logical or character, default TRUE (Auto guess new names). False: Skip renaming. A character vector of equal size as files wanted can also be given. Priority of renaming from the metadata is to check for unique names in the LibraryName column, then the sample_title column if no valid names in LibraryName. If new names found and still duplicates, will add "_rep1", "_rep2" to make them unique. If no valid names, will not rename, that is keep the SRR numbers, you then can manually rename files to something more meaningful.
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers

Value

character, full filepath of downloaded files

See Also

Other sra: download.SRA.metadata(), download.SRA(), install.sratoolkit(), rename.SRA.files()

ORFik documentation built on March 27, 2021, 6 p.m.