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Making Submission in SRA Submission Portal

Introduction

Check The Submission Portal Wizard provides a browser-based user interface for submitting SRA metadata as well as various options for uploading data files.

Exclamation point For better understanding of SRA submission process and SRA data organization please refer to SRA Metadata and Submission Overview.

Prerequisites

  • SRA accepts reads from high throughput sequencing platforms in specific formats (see the SRA File Format Guide for details). SRA does NOT accept assembled/consensus data or contigs.
  • For submissions of 1000 samples or less. If you have more than 1000 samples, please create multiple submissions with the same BioProject reference.
  • Files can be compressed using gzip or bzip2, and may be packaged in a tarball. Do not use zip! Packaging and/or compressing your files is not required.
  • Each submitted fastq file should be less than 100GB in size. If compressed files are larger than 100GB, please split them prior to submission.
  • Studies with more than 5TB of data should be split across multiple submissions, keeping each set of uploads under 5TB, and waiting for completion of each submission before uploading the next set of files. Submissions can be linked to the same BioProject to ensure all data are searchable with a single accession.
  • SRA does not accept submission of duplicate files and these submissions may be suppressed without warning. In addition, submitting duplicate data will lead to significant delays in processing of the submission. To update an existing record, do not resubmit the data files, instead contact the SRA helpdesk (sra@ncbi.nlm.nih.gov) for assistance.

Submitting

Log in to the SRA Submission Portal Wizard

On the Submission Portal Home Page https://submit.ncbi.nlm.nih.gov/ navigate to SRA or log in to the SRA Submission Portal Wizard directly.

Create new submission

Request a personal account folder to pre-upload your sequence data files (for the first time users) by clicking on the button Request preload folder.

Figure 1: Request personal account folder for file pre-upload

Request account folder for SRA

Requesting the account folder is recommended to allow for greater flexibility in file uploads. If you skip this step here, you will be given an opportunity to request the personal account folder later on the Files step of the submission.

Click the button New submission:

Figure 2: Create new SRA submission

Start new submission in SP for the first time
Exclamation point Your new submission receives a temporary submission ID in the form of SUB#. Please provide this ID when contacting SRA staff. This ID cannot be used as a reference in a publication.

Follow steps

Figure 3: SRA submission's steps including registration of new BioProject and BioSamples

SRA Portal Submission Steps

You may leave your submission at any step and return to finish it later.

1. Submitter

  • Check accuracy of your contact information and update it if necessary.
  • Create a group of collaborators if necessary.
  • Plan to use your primary email address in your communications with SRA staff.
  • Press the button Continue.

2. General Info

Select Yes in the first two sections of this step if you already registered your project and samples at the BioProject and BioSample Submission Portal Wizards. If you select No, the SRA Submission Wizard will ask you to create them, which may result in creating duplicates of your existing project and/or samples and this will lead to submission errors.

Provide the release date in the third section of this step. The default release date is set to Release immediately following processing.

You will be able to modify your release date later in the SRA User Interface.

3. Project Info

Exclamation point If you already have a project for your future publication, please do not create a separate project specifically for the SRA data.

Please refer to the SRA BioProject & Biosample Guide.

Tack In the SRA Submission Portal Wizard, registration of BioProject is simplified. The BioProject accession (PRJNA#) is assigned after the SRA submission is finished and is not required for SRA metadata.

Please read SRA specific guidelines here: BioProject & BioSample.

4. BioSample type

Select a package for your samples. Please refer to BioSample Packages.

If you determined that your human data must be submitted via dbGaP, please delete your current submission and refer to dbGaP Submission Guide.

Exclamation point Majority of SRA submissions require more than one sample. Make sure that every organism/metagenome, time point, tissue type or treatment type have their own sample.

5. BioSample attributes

Please do not use BioSamples that were registered in another user's account.

Select the most appropriate taxon for each organism/metagenome in the NCBI Taxonomy Browser. Providing the exact and most specific name for the organism/metagenome will simplify your BioSample submission.

For more information refer to BioSample documentation.

Refer to SRA Troubleshooting Guide to resolve common errors or warnings that occurred on this step.

6. SRA Metadata

Tack This step links your existing project (PRJNA#) and samples (SAMN#) with your SRA data.

There are two options for providing the SRA metadata:

  • Use built-in editor (sutable for submissions with fewer samples and provides some of required validation on the fly)
  • Upload a file (more convenient for large submissions)

Figure 4 - Built-in editor

Built-in editor in the SRA Submission Wizard

If you decided to upload a file with your metadata, you need to download the Excel spreadsheet template from the SRA metadata page.

Exclamation point Downloading new template ensures that you get the most current and correct version.

Instructions for metadata

  • If you just created project in the SRA wizard, leave the column bioproject_accession empty (if the column is present).

  • If you created samples previously, provide accessions in the form of SAMN# in the column sample_accession.

  • If you created samples in the SRA wizard, provide names of samples that you just created in the column sample_name. Please note that sample names must be unique within your entire account.

  • Each row in the template represents an EXPERIMENT. EXPERIMENT is a unique combination of sample + library + sequencing strategy + layout + instrument model. Each experiment should have a unique library_ID that is short and meaningful (like an ID you might use in lab).

  • Only one RUN per EXPERIMENT is allowed in the Submission Portal. When libraries are indeed identical (same combination of sample + library + strategy + layout + instrument model), all files should be placed in the same RUN. To do this simply enter the file names consecutively in the same row. PAIRED files must always be listed in the same row.

  • If uploading a bam file of reads aligned against a published NCBI assembly then enter the NCBI assembly name in the Reference assembly column. If your bam reads were aligned against a non-NCBI assembly then enter the filename of the custom reference in the Reference assembly column. Upload your non-NCBI assembly in fasta format (please do not compress the fasta file).

  • When submitting unaligned bam files (eg: PacBio *subreads.bam) please enter unaligned in the Reference assembly column.

  • If you archived your files with the tar utility, you must list the individual file names that are contained in the archive on your SRA metadata sheet (the one exception is a tar of .fast5 files for Nanopore native file submissions).

  • Provide exact file names (including extensions) in the filename columns. If uploading more than 8 files per sequencing library/run, please use the Excel spreadsheet instead of the embedded sheet as more filename# columns can be added to the Excel spreadsheet template as needed.

  • File names must be unique within a submission.

Click the button Continue.

Refer to SRA Troubleshooting Guide to resolve common errors or warnings that occurred on this step.

7. Files

Select one of the upload methods:

  • I have all files preloaded for this submission (best method for all submissions)
  • I will upload all the files now via HTTP/Aspera (suitable for submissions with a few small files)

Figure 5

Selection of file upload method in the SRA Submission Wizard

After you requested your personal account folder (either before starting your submission or on this step) AND checked the radiobutton "I have all files preloaded for this submission", the instructions and credentials will be provided on the page.

Detailed FTP and Aspera instructions can also be found here: SRA File Upload.

After you uploaded your files to your submission folder as instructed, please wait 10-15 minutes and click on the button Select Submission Folder.

Figure 6

Selection of the submission folder in the SRA Submission Wizard

After you finished uploading your files via Aspera/HTTP or selecting your submission folder, click the button Continue.

wait Unpacking and validation of compressed archives may take from several minutes to a few hours depending on their size and number.

Refer to SRA Troubleshooting Guide to resolve common errors or warnings that occurred on this step.

8. Overview

Please review your submission's summary and make sure that everything is correct including the release date.

At this stage, you can return to any step of your submission by clicking on the corresponding tabs.

Exclamation point Make sure that you clicked the button Submit

.

Exclamation point Once submitted, your submission is queued for processing. Allow at least 24 hours after submitting to receive feedback from SRA before contacting us. Note that if you created a BioProject or/and a BioSample submissions within the SRA Wizard, you will receive feedback from these databases first.

Downloading accessions

All your SRA submissions can be viewed on the SRA Submission Portal's home page: https://submit.ncbi.nlm.nih.gov/subs/sra/.

Figure 7

Finished SRA SP submission

Your submission's Overview page can be found by clicking on the link SUB# in the column Submission or by updating and entering the below link in your address bar:

https://submit.ncbi.nlm.nih.gov/subs/sra/[insert your SUB# here]/overview

Troubleshooting

For help with the SRA Submission Wizard refer to SRA Submission Portal Troubleshooting Guide.

Updating

Refer to the Update Guide: Updating SRA data.


Contact SRA staff

Before contacting SRA staff for assistance please visit our SRA Submission Portal Troubleshooting Guide.

Email sra@ncbi.nlm.nih.gov for help.

Exclamation point Please provide your submission's temporary ID in the form of SUB# in your messages.

Support Center

Last updated: 2022-07-25T16:25:50Z