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During the download, a temporary directory will be created in the location specified by the -t flag (in the example below, in /scratch/$USER) (Note: the old fastq-dump is being deprecated). You can download SRA fastq files using the fasterq-dump tool, which will download the fastq file into your current working directory by default. If you attempt to download non-ETL SRA data from AWS or GCP without the account information, you will see an error message along these lines:īucket is requester pays bucket but no user project provided. The user needs to establish account information, register it with the toolkit, and authorize the toolkit to pass this information to AWS or GCP to pay for egress charges. If requesting "original submission" files in bam or cram or some other format, they can ONLY be obtained from AWS or GCP and will require that the user provide a cloud-billing account to pay for egress charges. prefetch is the only SRAtoolkit tool that provides access to the original bams. Most sratoolkit tools such as fasterq-dump will pull ETL data from NCBI. In the case of ETL data, Sratoolkit tools on Biowulf will always pull from NCBI, because it is obviously nearer and there are no fees. Users who want access to the original bams can only get them from AWS or GCP today.
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NCBI maintains only ETL data online, while AWS and GCP have both ETL and original submission format. Two versions of the data exist: the original (raw) submission, and a normalized (extract, transform, load ) version. Amazon Web Services (= 'Amazon cloud' = AWS).
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You have to install and activate it before the Giveaway offer for the software is over.SRA Data currently reside in 3 NIH repositories: Please make sure to follow the instructions in the readme.txt file which is included in the package for proper activation. The giveaway will be valid for today day only.ĭon’t miss it.
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