NCBI SRA

README.md

Download files from SRA

This gist contains a few snippets of code to help automate downloading data using the NCBI SRA Toolkit.

1. Use the NCBI website to export a csv file with the details of experiment you wish to download. This file will contain just experiment accession numbers.
2. Use R to convert experiment accessiont to run accessions. Save these in runs.txt
3. Use this command to download all the files

  cat runs.txt | ./fetchall.sh

This will probably take a very long time so its a good idea to wrap this in a batch job script

fetchall.sh

while read p; do
  fastq-dump $p
done

sra.R

# Example showing how to translate experiment accessions into run accessions needed for download

library(SRAdb)
library(stringr)

# This downloads a 7gb sqlite file
sqlfile = getSRAdbFile()

dbcon = dbConnect('SQLite',sqlfile)

# Cephalopods.csv is a file of exported experiments from NCBI
exp_data = read.csv("Cephalopods.csv",stringsAsFactors=FALSE)
exp_acc = str_match(exp_data$Id,'accession:(.*)')[,2]

run_acc = sraConvert(exp_acc,'run',dbcon)[,2]

write.table(run_acc,file="runs.txt",quote=FALSE,row.names = FALSE)