To download metadata for each Run in your Entrez query click Send to on the top of the page, check theįile radiobutton, and select RunInfo in pull-down menu. SRA Run files do not contain any information about the metadata (sample information, etc.) linked to the data themselves. Downloading protected dataįor information on how to download dbGaP data see:ĭownload metadata associated with SRA data From the search result page Or the Data Access tab on the Run Browser or use any to get all available formats. You can look up the file type of the original files in either SRA in BigQuery
The -type command allows you to specify the type of file to download. Please refer to Download SRA sequence data using Amazon Web Services (AWS) You wish to use those instead of dumping standardized data from the archive. SRA has deposited original submitted files into a cloud bucket accessible via the prefetch command if sra extension in your fasterq-dump or sam-dump command:įasterq-dump -split-files SRR11180057 Downloading Original Submitted Files You can also avoid the prefetch step and download and convert the Run in one step by entering just the Run accession For example:įasterq-dump -split-files SRR11180057.sra Use this prefetch command to download the Runs from the previous example in SRA format.įasterq-dump and sam-dump are also part of the SRA toolkit and can be used to convert the prefetched Runsįrom compressed SRA format to fastq or sam format. Prefetch can be used to correct and finish an incomplete Run download.
This program downloads Runs (sequence files in the compressed SRA format) and all additionalĭata necessary to convert the Run from the SRA format to a more commonly used format. Please make sure you are running the most recent release of the toolkit as older versions may not be compatible with more recently loaded data or the most current network protocols.
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