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Submitting Read Data to NCBI SRA

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Brant Faircloth edited this page Jul 18, 2017 · 7 revisions 
Title:       Submitting Read Data to NCBI SRA     
Project:     faircloth-lab documentation project  
Author:      Carl Oliveros, Brant Faircloth  
Affiliation: faircloth-lab  
Web:         http://faircloth-lab.org  
Date:        22 June 2017

Purpose

These are the steps to follow to submit raw-read (fastq) data from sequencing runs to the NCBI Sequence Read Archive (SRA). There are several components parts to this document. These consist of:

  1. Registering a BioProject
  2. Registering BioSamples
  3. Submitting data to NCBI SRA

I've broken this document into component parts, because sometimes you might want to create a BioProject (giving you a BioProject accession number to use in your publications) before you have time to upload all of your data. That said, our laboratory policy is to upload all the data, all the time prior to publication (and usually prior to making a paper available as a pre-print).

Steps

  1. Register an NCBI BioProject (if you have not already done so)

  2. Register NCBI BioSamples for a BioProject (if you have not already done so)

  3. Once your BioSamples are processed, you should receive a tab delimited file with accession numbers for each of your samples. Before you start the next steps, make sure you have installed the Aspera connect plugin. This plugin will allow you to use the browser to select raw read files from your computer to upload.

  4. Log in to the NCBI submissions portal, and click on the SRA link:

    ncbi-sra

  5. Click on the "New Submission" link at the top of the page.

    ncbi-sra-new-submission

  6. As with the previous steps, verify the info on the Submitter tab. Click Continue.

  7. On the General info tab, enter your BioProject accession number and select your project. Also provide a Release Date. Select No for "Do you want to create new BioSamples for this submission?" because we already have created them in the previous step. Click Continue.

    ncbi-sra-general-info

  8. On the SRA metadata tab, download the SRA metadata Excel template.

    ncbi-sra-metadata

  9. Follow the instructions on the worksheet and fill it in. Comments on top of the fields provide a useful description. Use the following values:

    Field Comments
    BioProject accession There should be only one for all rows
    BioSample accession There should be a unique accession for each row. Copy this info from the text file sent to you.
    library ID Use something like "Species-genus-Institution-Accesssion"
    title Use something like "UCE target enrichment of Species-genus-Institution-Accesssion: muscle/liver tissue" or something similar
    library strategy WGS
    library source Genomic
    library selection Hybrid selection
    library layout paired
    platform Illumina
    instrument_model your Illumina model
    design_description Copy the library prep description from the methods of your paper and paste here. You may have to make this a bit concise. You can't have more than 1 paragraph.
    filetype fastq
    filename filename of the read1 file (do not include paths)
    filename2 filename of the read2 file (do not include paths)

    Once completely filled in, save the appropriate tab of the worksheet as a tab delimited file and upload onto the SRA metadata tab. Click Continue.

  10. On the Files tab, use the Browse button to select the relevant files to upload. You can do this in batches, if you wish.

    ncbi-sra-browse-tab

    When uploading files, make sure that the progress bars are visible as below. Even if files are uploading via the Aspera Connect plugin but the progress bars are not visible, you are NOT uploading files.

    ncbi-sra-progress-bars

  11. Click on the Autofinish submission button and then click Continue. If no errors are reported, the submission will be in process.

  12. After processing, you should receive an email from NCBI that looks like the following:

    Dear XXXXXXX,

This is an automatic acknowledgment that your recent submission to SRA database
has been successfully processed and will be released on the date specified.

Please reference SRP078335 in your publication.

SRA accession: SRP078335
Temporary Submission ID: SUB1681796
Release date: 2017-07-01

Your SRA records will be accessible with the following link after the indicated
release date: http://www.ncbi.nlm.nih.gov/sra/SRP078335

Send questions and update requests to [email protected]; include the SRA
accession SRP078335 in any correspondence.

Regards,

NCBI SRA Submissions Staff
Bethesda, Maryland USA
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