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Import Files from SRA with the SRA Toolkit

Description:

Now that we have a list of accessions, we can use our first application. The sra-tools prefetch app will allow us to import data from the SRA. All of the applications we will be using in the Discovery Environment have been collected together. You may access them by going to the Collections icon in the Discovery Environment. Select the All Collections view and scroll to find the Plant Bioinformatics Vol. 3 Tutorial collection. You may also search for any application by name in the Apps catalogue.

Input Data:

Input Description Example
SRR_Acc_List.txt Accession list from the SRA SRR_Acc_List

Use 'sra-tools prefetch' App to Import SRA Data

  1. In the , go to Apps and search for sra-tools prefetch. You can use this direct link: sra-tools prefetch app

Note

All applications used in this tutorial are collected in the Plant Bioinformatics Vol. 3 Tutorial collection - See Collections in the Discovery Environment.

  1. In Analysis Info you can name this analysis and provide any comments (optional). Under Output folder, navigate to the rna-seq-tutorial folder created earlier. Your outputs will automatically be placed in this folder); click Next.

Tip

For future analyses, from the Settings icon in the Discovery Environment under Default analysis output folder you can change the default setting for your outputs. This can be useful when you will be doing several analyses and you want them to go to a folder other than your analyses folder (the default setting).

  1. In Parameters under Accession list browse to your rna-seq-tutorial folder and enter the metadata folder; select SRR_Acc_List.txt as input; click Next.
  2. In Advanced Settings (optional), each application in the Discovery Environment has a 'Resource Requirements' option. These are some minimal computational resources that you can choose for the application. When the Discovery Environment launches an analysis job, it may be run on computing hardware of various capabilities (according to what "nodes" are available to accept the job). App developers may have set minimums here but you may choose to make adjustments. If you don't know which minimums to choose, you can ignore these options. If you do run into errors, you can contact CyVerse support. Also contact support if the resources you need for an app do not appear in the list of options; CyVerse can increase these minimums. We will not make any changes; click Next.
  3. In Review and Launch, click Launch Analysis to begin the analysis job. You will get notification(s) in the Discovery Environment about the status of the job, including an email (by default preferences settings) when the job is complete.
  4. Click on Analyses view to see the current status of the job; you can also click on the Analyses icon to navigate to this section. When the job is complete, you can click on the folder icon next to the analyses name to browse the results. You may need to Refresh to see the current job status. This job will vary on connection speed between the CyVerse servers and NCBI. This job is estimated to take about 15-30 minutes.
  5. When the job has status Completed, navigate to the output. The resulting output will be 12 folders (one for each accession), each containing a single SRA file (e.g., SRR9666131.sra, SRR9666132.sra ... ). There will also be a logs folder containing output logs from the CyVerse Discovery Environment analysis.

Output/Results

Output Description Example
SRA files (SRR9666131.sra, SRR9666132.sra ...) These are sequence data in the SRA format SRA files

Description of output and results

The imported SRA files should be validated for their integrity - these are large files and we want to make sure the data has not be corrupted. We will do this integrity check in the next step.

Last update: 2022-11-28