how to use fastq-dump

1. Google 'GSE40419' (GEO accession number)

2. Look for 'BioProject' or 'SRA' ID (RJNA173917 or ERP001058)

3. Go to 'SRA Run Selector' 

4. Enter "RJNA173917" or "ERP001058" in the search.

5. Choose samples to download.

6. Click 'RunInfo Table', save it to a file, and extract "SRA_sample" column,

or download 'Accession List', and save it.

Resulting file should look like below ( a single column list of accession numbers).

 
$ cat > accession

ERR164564
ERR164569
ERR164570
ERR164580
ERR164556
ERR318891
ERR164600
ERR164601

 
7. Run 'fastq-dump' to download the fastq files.

$ cat accession | while read l; do prefetch $l && vdb-validate $l && fastq-dump --split-3 --gzip $l & done