Downloading from the SRA · Kylepedia

Downloading from the SRA

How to download SRA fastq files and metadata

I find the documentation for the SRA fairly confusing, and performing simple tasks such as download files from the linux CLI can be tricky.

Here’s how to download SRA fastq files and metadata from the CLI. This requires the SRA Toolkit for downloading FastQ files. http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

For PE reads, use the –split-files option. Otherwise, the forward and reverse reads will be concatenated together.

fastq-dump --split-files SRR1561863

To download the metadata for SRR1561863, use wget. The following commands will download the metadata to xml or csv.

wget -O ./SRR1561863_info.csv 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=SRR1561863' wget -O ./SRR1561863_info.xml 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=xml&term=SRR1561863'

SRR1561863 can be replaced with the desired ascension number.

Sources:

https://nsaunders.wordpress.com/2011/12/22/sequencing-for-relics-from-the-sanger-era-part-1-getting-the-raw-data/