get_fastqs: Download and RNA-seq fastq data from EBI

In alexvpickering/GEOfastq: Downloads ENA Fastqs With GEO Accessions

Description

First tries to get RNA-Seq fastq files from EBI.

Usage

get_fastqs(srp_meta, data_dir, method = c("ftp", "aspera"), max_rate = "1g")

Arguments

srp_meta	data.frame with SRP meta info. Returned from crawl_gsms.
data_dir	Path to folder that fastq files will be downloaded to. Will be created if doesn't exist.
method	One of 'aspera' or 'ftp'. 'aspera' is generally faster but requires the ascp command line utility to be on your path and in the authors experience frequently stalls.
max_rate	Used when method = 'aspera' only. Sets the target transfer rate. The default is '300m'.

Value

Named vector of integer return codes from ascp or download.file. Names are SRR runs.

Examples

gsm_name <- 'GSM3926903'
srp_meta <- crawl_gsms(gsm_name)
data_dir <- tempdir()
res <- get_fastqs(srp_meta, data_dir)

alexvpickering/GEOfastq documentation built on Oct. 11, 2021, 6:44 p.m.