7  Download GEO data

7.1 Download SRA files

  • Download latest SRA-tool
wget --output-document sratoolkit.tar.gz\
http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
  • sratoolkit.tar.gz file will be downloaded.
tar -xvzf sratoolkit.tar.gz

export PATH=$PATH:/home/basu/sratoolkit.3.0.1-ubuntu64/bin
  • Check whether the tool is working or not by executing the following command
prefetch -h

  • Now let us download the following data from GEO. Transcriptional profiling of adult retinal ganglion cells during optic nerve regeneration [GSE142881: RGC injury dataset]

  • Create a script file with vim editor download.sh and paste the following script into that.

vim download.sh
Note

vim download.sh → insert (press I in your keyboard) → esc → :wq → chmod +x download.sh

Bash Script

#!/bin/sh
# Downloading the SRA files using Prefetch command
for i in $(seq 10821165 10821205)
do
prefetch -v SRR$i --max-size 50G
done
chmod +x download.sh
  • Execute the script by typing
nohup bash download.sh

7.2 Convert .sra file to .fastq files

mkdir fastq/
  • Make another script loop.sh to convert .sra file to .fastq file
vim loop.sh

Bash script

#!/bin/sh
# convert using fasterq-dump command
for i in $(seq 10821165 10821205)
do
fasterq-dump --split-files --skip-technical -e 16 SRR$i --outdir fastq
done
chmod +x loop.sh
nohup bash loop.sh

7.3 Make gzip compression of the fastq files

cd fastq/
gzip *.fastq
Note

The next step would be checking the quality of the fastq files. See Chapter 4 for the details of fastqc commands and quality check. I would recommend to refer to that section before proceeding to quality control of fastq data.

  • In the next section we are going to install packages and dependencies.