Tools for downloading and processing data from the Sequence Read Archive (SRA)
Identify files to download from the SRA search interface, click the "Send to" dropdown menu , select "File" as the destination, and set "Format" to "RunInfo".
Copy the SraRunInfo.csv file into the current working directory. Optionally,
rename the file with a more descriptive title and update config.json to point
to the new file name. Add or remove lines from the run info file to change which
files to download and extract.
Download the source code for sratools.
git clone https://github.com/EichlerLab/sratools.git
cd sratools
Setup the working environment by adding Anaconda, Aspera, and SRA Toolkit to the environment.
. config.sh
Download all SRA files grouped by sample id and run accession.
snakemake sra
Extract compressed FASTQs from the SRA files.
snakemake fastq
If the SRA run information is missing proper annotations for sex or sample name for a specific sample, an override value for both of these attributes can be specified through the Snakemake configuration interface.
snakemake sra --config sex=F sample=Kamilah