get_ebi_fastqs {GEOfastq}R Documentation

Download fastqs from EBI

Description

Much faster to use aspera than ftp

Usage

get_ebi_fastqs(
  srp_meta,
  srr_name,
  data_dir,
  method = c("ftp", "aspera"),
  max_rate = "300m"
)

Arguments

srp_meta

data.frame with SRP meta info. Returned from crawl_gsms.

srr_name

Run accession as string.

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

Integer return code from ascp or download.file.

[Package GEOfastq version 1.2.0 Index]