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<h1 id="making-submission-in-sra-submiss">Making Submission in SRA Submission Portal</h1>
<div class="toc">
<ul>
<li><a href="#introduction">Introduction</a></li>
<li><a href="#prerequisites">Prerequisites</a></li>
<li><a href="#submitting">Submitting</a><ul>
<li><a href="#log-in-to-the-sra-submission-por">Log in to the SRA Submission Portal Wizard</a></li>
<li><a href="#create-new-submission">Create new submission</a></li>
<li><a href="#follow-steps">Follow steps</a><ul>
<li><a href="#1-submitter">1. Submitter</a></li>
<li><a href="#2-general-info">2. General Info</a></li>
<li><a href="#3-project-info">3. Project Info</a></li>
<li><a href="#4-biosample-type">4. BioSample type</a></li>
<li><a href="#5-biosample-attributes">5. BioSample attributes</a></li>
<li><a href="#6-sra-metadata">6. SRA Metadata</a></li>
<li><a href="#7-files">7. Files</a></li>
<li><a href="#8-overview">8. Overview</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#downloading-accessions">Downloading accessions</a></li>
<li><a href="#troubleshooting">Troubleshooting</a></li>
<li><a href="#updating">Updating</a></li>
<li><a href="#contact-sra-staff">Contact SRA staff</a></li>
</ul>
</div>
<h2 id="introduction">Introduction</h2>
<p><img src="/core/assets/sra/images/galka.png" alt="Check" height="20" />
<a title="Unified Submission Portal" target="_blank" href="https://submit.ncbi.nlm.nih.gov/subs/sra/">The Submission Portal Wizard</a> provides a browser-based user interface for submitting SRA metadata as well as various options for uploading data files.</p>
<p><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> For better understanding of SRA submission process and SRA data organization please refer to <a target="_blank" title="SRA Metadata and Submission Overview, new window" href="/sra/docs/submitmeta">SRA Metadata and Submission Overview</a> and see our 'How to Submit' video tutorial.<br />
  </p>
<div align="center"><iframe src="https://www.youtube.com/embed/PTg9Ru68fc0" width="452" height="254" title="How to Submit to SRA, A Beginner's Guide" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen=""></iframe></div>
<p>  </p>
<h2 id="prerequisites">Prerequisites</h2>
<ul>
<li>SRA accepts reads from high throughput sequencing platforms in specific formats (see the SRA <a target="_blank" title="The SRA File Format Guide" href="/sra/docs/submitformats/">File Format Guide</a> for details). SRA does NOT accept assembled/consensus data or contigs. </li>
<li>For submissions of 1000 samples or less. If you have more than 1000 samples, please create multiple submissions with the same BioProject reference.</li>
<li>Files can be compressed using <strong>gzip</strong> or <strong>bzip2</strong>, and may be packaged in a tarball. Do not use <strong>zip</strong>! Packaging and/or compressing your files is not required. </li>
<li>Each submitted fastq file should be less than 100GB in size. If compressed files are larger than 100GB, please split them prior to submission.</li>
<li>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. </li>
<li>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. </li>
</ul>
<h2 id="submitting">Submitting</h2>
<h3 id="log-in-to-the-sra-submission-por">Log in to the SRA Submission Portal Wizard</h3>
<p>On the Submission Portal Home Page <a target="_blank" title="Submission Portal SRA, new window" href="https://submit.ncbi.nlm.nih.gov/">https://submit.ncbi.nlm.nih.gov/</a> navigate to <strong>SRA</strong> or log in to <a target="_blank" title="Submission Portal SRA, new window" href="https://submit.ncbi.nlm.nih.gov/subs/sra">the SRA Submission Portal Wizard</a> directly.</p>
<h3 id="create-new-submission">Create new submission</h3>
<p>Request a personal account folder to pre-upload your sequence data files (<strong>for the first time users</strong>)
by clicking on the button <span class="greenbutton">Request preload folder</span>. </p>
<p>Figure 1: Request personal account folder for file pre-upload </p>
<div class="shadowing"><img src="/core/assets/sra/images/request-preupload-folder.png" alt="Request account folder for SRA" width="600" /></div>
<p>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 <strong>Files</strong> step of the submission.</p>
<p>Click the button <span class="greenbutton">New submission</span>: </p>
<p>Figure 2: Create new SRA submission</p>
<div class="shadowing"><img src="/core/assets/sra/images/new-sub-SP-creds-instr.png" alt="Start new submission in SP for the first time" width="600" /></div>
<div class="warning-message"> <img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> Your new submission receives a
temporary submission ID in the form of <span class="bold">SUB#</span>. Please provide this ID when contacting SRA staff.
<span class="bold">This ID cannot be used as a reference in a publication.</span></div>
<h3 id="follow-steps">Follow steps</h3>
<p>Figure 3: SRA submission's steps including registration of new BioProject and BioSamples</p>
<div class="shadowing"> <img src="/core/assets/sra/images/sra-8-steps.png" alt="SRA Portal Submission Steps" width="600" /></div>
<p>You may leave your submission at any step and return to finish it later.</p>
<h4 id="1-submitter">1. <strong>Submitter</strong></h4>
<ul>
<li>Check accuracy of your contact information and update it if necessary.</li>
<li>Create a group of collaborators if necessary. </li>
<li>Plan to use your primary email address in your communications with SRA staff. </li>
<li>Press the button <span class="greenbutton">Continue</span>. </li>
</ul>
<h4 id="2-general-info">2. <strong>General Info</strong></h4>
<p>Select <strong>Yes</strong> 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 <strong>No</strong>, 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.</p>
<p>Provide the release date in the third section of this step. The default release date is set to <strong>Release immediately following processing</strong>. </p>
<p>You will be able to <a title="Change release date" targer="_blank" href="/sra/docs/submitsra/">modify your release date</a> later in the SRA User Interface.</p>
<h4 id="3-project-info">3. <strong>Project Info</strong></h4>
<div class="warning-message"><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> If you already have
a project for your future publication,
please <span class="bold">do not create a separate project specifically for the SRA data</span>.</div>
<p>Please refer to <a target="_blank" title="How to submit BioProject and BioSample" href="/sra/docs/submitbio">the SRA BioProject &amp; Biosample Guide</a>. </p>
<p><img src="/core/assets/sra/images/tack.png" alt="Tack" height="20" /> In the SRA Submission Portal Wizard, registration
of BioProject is simplified. The BioProject accession (<strong><code>PRJNA#</code></strong>) is assigned after
the SRA submission is finished and is not required for SRA metadata.</p>
<p>Please read SRA specific guidelines here:
<a target="_blank" title="Submitting BioProject and BioSample" href="/sra/docs/submitbio">BioProject &amp; BioSample</a>.</p>
<h4 id="4-biosample-type">4. <strong>BioSample type</strong></h4>
<p>Select a package for your samples. Please refer to <a target="_blank" title="BioSample Packages" href="/biosample/docs/packages/">BioSample Packages</a>. </p>
<p>If you determined that your human data must be submitted via dbGaP, please delete your current submission and
refer to <a target="_blank" title="dbGaP Submission Guide" href="/sra/docs/submitdbgap">dbGaP Submission Guide</a>. </p>
<div class="warning-message"><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> Majority of SRA submissions
require <span class="bold">more than one sample</span>. Make
sure that every organism/metagenome, time point, tissue type or treatment type have their own sample.
</div>
<h4 id="5-biosample-attributes">5. <strong>BioSample attributes</strong></h4>
<p>Please do not use BioSamples that were registered in another user's account.</p>
<p>Select the most appropriate taxon for each organism/metagenome in <a title="Taxonomy browser" target="_blank" href="/taxonomy/">the NCBI
Taxonomy Browser</a>. Providing the exact and most specific name for the organism/metagenome will simplify your BioSample submission. </p>
<p>For more information refer to <a target="_blank" title="BioSample documentation" href="/biosample/docs/">BioSample documentation</a>. </p>
<p>Refer to <a target="_blank" title="SRA Troubleshooting Guide" href="/sra/docs/submitspfiles">SRA Troubleshooting Guide</a> to resolve common
errors or warnings that occurred on this step.</p>
<h4 id="6-sra-metadata">6. <strong>SRA Metadata</strong></h4>
<div class="warning-message"><img src="/core/assets/sra/images/tack.png" alt="Tack" height="20" /> This step links your existing project
(<span class="bold">PRJNA#</span>) and samples (<span class="bold">SAMN#</span>) with your SRA data.
</div>
<p>There are two options for providing the SRA metadata: </p>
<ul>
<li><strong>Use built-in editor</strong> (sutable for submissions with fewer samples and provides some of required validation on the fly)</li>
<li><strong>Upload a file</strong> (more convenient for large submissions)</li>
</ul>
<p>Figure 4 - Built-in editor</p>
<div class="shadowing"> <img src="/core/assets/sra/images/built-in-editor.png" alt="Built-in editor in the SRA Submission Wizard" width="600" /></div>
<p>If you decided to upload a file with your metadata, you need to download the Excel spreadsheet template from the <strong>SRA metadata</strong> page.</p>
<div class="warning-message"><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> Downloading
new template ensures that you get the most current and correct version.</div>
<h3 class="green">Instructions for metadata</h3>
<ul>
<li>
<p>If you just created project in the SRA wizard, leave the column <strong>bioproject_accession</strong> empty (if the column is present). </p>
</li>
<li>
<p>If you created samples previously, provide accessions in the form of <strong>SAMN#</strong> in the column <strong>sample_accession</strong>. </p>
</li>
<li>
<p>If you created samples in the SRA wizard, provide <strong>names of samples</strong> that you <strong>just created</strong> in the column <strong>sample_name</strong>. Please note that sample names must be <strong>unique within your entire account</strong>. </p>
</li>
<li>
<p>Each row in the template represents an EXPERIMENT. <strong>EXPERIMENT</strong> is a unique combination of <strong><em>sample + library + sequencing strategy + layout + instrument model</em></strong>. Each experiment should have a <strong>unique</strong> <strong><em>library_ID</em></strong> that is short and meaningful (like an ID you might use in lab). </p>
</li>
<li>
<p>Only one RUN per EXPERIMENT is allowed in the Submission Portal. When libraries are indeed identical (same combination of <strong><em>sample + library + strategy + layout + instrument model</em></strong>), all files should be placed in the same RUN. To do this simply enter the file names consecutively in the same row. <strong>PAIRED</strong> files must always be listed in the same row. </p>
</li>
<li>
<p>If uploading a <strong>bam</strong> file of reads aligned against a published NCBI assembly then enter the NCBI assembly name in the <strong>Reference assembly</strong> column. If your bam reads were aligned against a non-NCBI assembly then enter the filename of the custom reference in the <strong>Reference assembly</strong> column. Upload your non-NCBI assembly in fasta format (please do not compress the <strong>fasta</strong> file). </p>
</li>
<li>
<p>When submitting unaligned bam files (eg: PacBio <code>*subreads.bam</code>) please enter <strong>unaligned</strong> in the <strong>Reference assembly</strong> column. </p>
</li>
<li>
<p>If you archived your files with the <strong>tar</strong> 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). </p>
</li>
<li>
<p>Provide <strong>exact file names</strong> (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
<strong>filename#</strong> columns can be added to the Excel spreadsheet template as needed. </p>
</li>
<li>
<p>File names must be <strong>unique</strong> within a submission. </p>
</li>
</ul>
<p>Click the button <span class="greenbutton">Continue</span>.</p>
<p>Refer to <a target="_blank" title="SRA Troubleshooting Guide" href="/sra/docs/submitspfiles">SRA Troubleshooting Guide</a> to resolve common
errors or warnings that occurred on this step. </p>
<h4 id="7-files">7. <strong>Files</strong></h4>
<p>Select one of the upload methods: </p>
<ul>
<li><strong>I have all files preloaded for this submission</strong> (best method for all submissions)</li>
<li><strong>I will upload all the files now via HTTP/Aspera</strong> (suitable for submissions with a few small files)</li>
</ul>
<p>Figure 5 </p>
<div class="shadowing"> <img src="/core/assets/sra/images/request-upload-folder-on-files-step-2.png" alt="Selection of file upload method in the SRA Submission Wizard" width="600" /></div>
<p>After you requested your personal account folder (either before starting your submission or on this step) AND checked the radiobutton <strong>"I have all files preloaded for this submission"</strong>, the instructions and credentials will be provided on the page. </p>
<p>Detailed FTP and Aspera instructions can also be found here: <a target="_blank" title="SRA Submission Portal Wizard" href="/sra/docs/submitfiles/">SRA File Upload</a>.</p>
<p>After you uploaded your files to your submission folder as instructed, please wait 10-15 minutes and click on the button <span class="greenbutton">Select Submission Folder</span>.</p>
<p>Figure 6</p>
<div class="shadowing"> <img src="/core/assets/sra/images/preupload-folder-selected.png" alt="Selection of the submission folder in the SRA Submission Wizard" width="600" /></div>
<p>After you finished uploading your files via Aspera/HTTP or selecting your submission folder, click the button <span class="greenbutton">Continue</span>.</p>
<div class="patience"><img src="/core/assets/sra/images/watch.png" alt="wait" width="20" /> Unpacking and validation of
compressed archives may take from several minutes to a few hours depending on their size and number.</div>
<p>Refer to <a target="_blank" title="SRA Troubleshooting Guide" href="/sra/docs/submitspfiles">SRA Troubleshooting Guide</a> to resolve common
errors or warnings that occurred on this step. </p>
<h4 id="8-overview">8. <strong>Overview</strong></h4>
<p>Please review your submission's summary and make sure that everything is correct including <strong>the release date</strong>. </p>
<p>At this stage, you can return to any step of your submission by clicking on the corresponding tabs. </p>
<div class="warning-message"><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" />
Make sure that you clicked the button <span class="greenbutton">Submit</span></div>
<p>.</p>
<p><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> 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.</p>
<h2 id="downloading-accessions">Downloading accessions</h2>
<p>All your SRA submissions can be viewed on the SRA Submission Portal's home page: <a href="https://submit.ncbi.nlm.nih.gov/subs/sra/">https://submit.ncbi.nlm.nih.gov/subs/sra/</a>.</p>
<p>Figure 7 </p>
<div class="shadowing">
<img src="/core/assets/sra/images/finished-SRA-SP-submission.png" alt="Finished SRA SP submission" width="700" /></div>
<p>Your submission's <strong>Overview page</strong> can be found by clicking on the link <strong>SUB#</strong> in the column <strong>Submission</strong> or by updating and entering the below link in your address bar:</p>
<p><strong><code>https://submit.ncbi.nlm.nih.gov/subs/sra/[insert your SUB# here]/overview</code></strong></p>
<h2 id="troubleshooting">Troubleshooting</h2>
<p>For help with the SRA Submission Wizard refer to <a target="_blank" title="Troubleshooting SRA submission in Submission Portal" href="/sra/docs/submitspfiles">SRA Submission Portal Troubleshooting Guide</a>.</p>
<h2 id="updating">Updating</h2>
<p>Refer to the Update Guide: <a target="_blank" title="Updating SRA data" href="/sra/docs/submitupdate">Updating SRA data</a>. </p>
<hr />
<h2 id="contact-sra-staff">Contact SRA staff</h2>
<p>Before contacting SRA staff for assistance please visit our <a target="_blank" title="Troubleshooting SRA submission in Submission Portal" href="/sra/docs/submitspfiles">SRA Submission Portal Troubleshooting Guide</a>. </p>
<p>Email <a href="mailto:sra@ncbi.nlm.nih.gov">sra@ncbi.nlm.nih.gov</a> for help. </p>
<p><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> Please provide your submission's temporary ID in the form of <strong><code>SUB#</code></strong> in your messages. </p>
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<h2 data-heading="h2" data-no-toc="true">Getting Started</h2>
<ul>
<li><a title="SRA Getting Started" href="/sra/docs/">Getting Started</a></li>
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<h2 data-heading="h2" data-no-toc="true">Submitting Data to SRA</h2>
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<li><a title="Submitting SRA data for dbGaP project" href="/sra/docs/submitdbgap">Submitting for dbGaP</a></li>
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