Here for demo purpose, we just download the test key from NCBI: Second, once you've obtained the key file, you may continue to follow the step 3 ![]() SRA contains a lot of protected data that requires extra steps to gain access to them.įirst, you need to follow the link, to get a repository key, called 'NGC' key file. out/PRJNA525241 - store the fastq files for PRJNA525241.out/sra - store the sra files for PRJNA525241.qlog/sra_example.poxxxxxxx # 'xxxxxxx' stands for job number.cd qsub # get into the qsub script locationĪfter the above job's completion, there will be two files in qlog/ looks like: You can write a qsub script to download data for multiple accessions. Please refer to NCBI SRA toolkit documentation website for more information. There are a lot more functions and utlities included in this tool to assist sequence retrival and process. The above command will output on screen as recorded in out/fasterq-dump.out.Īnd the downloaded sequence files can be found in data/: fasterq-dump -p -t /scratch/$USER -outdir data SRR030257 2>&1 | tee out/fasterq-dump.out rm -rf data # make sure data/ doesn't exist It's a good habit to specify the temporary folder in scratch and store the downloaded sequence data in dedicated data folder: So the above sequence download will need 169M*4=676M for output, and another 676M for temporary files.Įx2: To download data from NCBI SRA repository, run the following command. * As a rule of thumb, the fasterq-dump guide suggests getting the size of the accession using 'vdb-dump', then estimating 4x for the output and 4x for the temp files. vdb-dump -info SRR030257 -output-file out/vdb-dump_info.out # this will store output to file vdb-dump -info SRR030257 # this will show result on the screen Before run any SRA ulitilies, first to load sratoolkit to make them available:Ĭommandline Examples: Ex1: To check space requirement for download target: To view all available SRAToolkit versions on SCC, execute:Ģ. dbGaP -d dedicated folder to give example on how to download dbGap data.ġ.qlog -d dedicated folder to store all qsub output logs. ![]()
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