Data Access: Downloading SRA and FastQ data in R using SRAdb fasp/ftp protocols

Beatriz Manso
2022-02-23

Introduction

DNA sequences of short reads generated by high throughput sequencing are stored in the Sequence Read Archive (SRA), a bioinformatics database.

SRA is an inter-institutional collaboration among NCBI SRA, EBI ENA and DDBJ DRA.

Using SRA, organisms are arranged hierarchically based on sequence and are classified into six categories:

Methods

1. Set Working directory

setwd("C:/Users/manso/OneDrive - University of West London/MSc Bioinformatics - UWL/7.MSc Bioinformatics Project/W2 - Sample size and power analysis/practical")

2. Instaling necessary packages

if (!requireNamespace("BiocMansger", quietly=TRUE))
  install.packages("BiocManager", repos ="http://cran.us.r-project.org")

package 'BiocManager' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\manso\AppData\Local\Temp\RtmpeQDety\downloaded_packages
BiocManager::install("SRAdb")

3. Load libraries

library(SRAdb)

4. Download the SRAmetadb sqlite database

This code chunk will only download if the file does not exist. It can take a while to download(~2.4GB zip file)

if( ! file.exists('SRAmetadb.sqlite.gz') ) {
  sra_dbname <- getSRAdbFile()
  } else { 
  sra_dbname <- 'SRAmetadb.sqlite.gz'
}
sra_dbname <- file.path(system.file('extdata', package='SRAdb'), 'SRAmetadb_demo.sqlite')

#Connect to the database
sra_con <- dbConnect( dbDriver("SQLite"), sra_dbname )

5. List fasp addresses of sra files associated with “SRR” ID

listSRAfile( c("SRR000648","SRR000657"), sra_con, fileType = 'sra', srcType='fasp')

        run     study    sample experiment
1 SRR000648 SRP000098 SRS000290  SRX000122
2 SRR000657 SRP000098 SRS000290  SRX000122
                                                                                                    fasp
1 anonftp@ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR000/SRR000648/SRR000648.sra
2 anonftp@ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR000/SRR000657/SRR000657.sra

6. Download SRA files using fasp protocol

ascpCMD <- 'ascp -QT -l 300m -i /usr/local/aspera/connect/etc/asperaweb_id_dsa.putty'

SRAFiles <- getSRAfile( c("SRR000648","SRR000657"), sra_con, 
                        fileType = 'sra', srcType = 'fasp', ascpCMD = ascpCMD )

-T : disable encryption for maximum throughput -l : set the target transfer rate in kbps -i : to specify a private key file.

7. Get information about the fastQ files for sample accession IDs

getFASTQinfo( in_acc = c("SRR000648","SRR000657"), sra_con, srcType = 'fasp' )

        run submission     study    sample experiment
1 SRR000648  SRA000241 SRP000098 SRS000290  SRX000122
2 SRR000657  SRA000241 SRP000098 SRS000290  SRX000122
                                                                        fasp
1 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR000/SRR000648/SRR000648.fastq.gz
2 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR000/SRR000657/SRR000657.fastq.gz

8. Download FASTQ files using ftp protocol

getFASTQfile( in_acc = c("SRR000648","SRR000657"), sra_con, destDir = getwd(),
              srcType = 'ftp', makeDirectory = FALSE, method = 'curl', ascpCMD = NULL)

        run submission     study    sample experiment
1 SRR000648  SRA000241 SRP000098 SRS000290  SRX000122
2 SRR000657  SRA000241 SRP000098 SRS000290  SRX000122
                                                                     ftp
1 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR000/SRR000648/SRR000648.fastq.gz
2 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR000/SRR000657/SRR000657.fastq.gz

The sra or sra-lite data files are downloaded from NCBI SRA and the fastq files are downloaded from EBI ENA.

The files are donloaded in to the working directory.

dbDisconnect( sra_con )