Go to the place where your Raw data is deposited

• Illumina basespace
• SRA-Sequence Read Archive
• ENA -European Nucleotide Archive
• DDBJ-DNA Databank of Japan

To Download FastQ files

Data for this tutorial were deposited to SRA. We will visualize this on your local computer

• Manuscript: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245787/
• Go to SRA: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP049724

Download the RunInfoTable and Accession List by clicking on the buttons

Going back to OSC

cd $wd/RNASeq_Gene_Expression_Analysis/Metadata

Create a table called 'SRA_accession_tutorial.txt'

# open an empty file using the nano editor
nano SRA_accession_tutorial.txt

#Paste the name of the accessions from the file SRR_Acc_List.txt
SRR1649142
SRR1649141
SRR1649140
SRR1649133
SRR1649132
SRR1649131
# The CTRL+X and hit "enter" to confirm the changes to the file

# Load SRAtoolkit in Owens
module load sratoolkit/2.9.0

# Download each FastQ file using sratoolkit
for acn in $(cat SRA_accession_tutorial.txt)
do
fastq-dump --outdir ../RAW_Reads/ --split-files --gzip $acn
done