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<div class="search"><form method="get" action="/sra/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="sra" selected="selected">SRA</option><option value="nuccore">Nucleotide</option><option value="books">Books</option><option value="pubmed" class="last">PubMed</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search SRA" value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="isEnabled:false,disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'yes'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div></form><ul class=" inline_list searchlinks"><li>
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<a title="SRA Submission Quick Start" href="/sra/docs/submit">Submission Quick Start</a></li>
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<a title="How to use SRA in the cloud" href="/sra/docs/sra-cloud">SRA in the Cloud</a>
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<a title="Archive Documentation" href="/sra/docs/sra-data-storage-model/">Archive Documentation</a>
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<li><a title="Data Storage Model" href="/sra/docs/sra-data-storage-model/">Data Storage Model</a></li>
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<li><a title="Root Cause Analysis: Summary and Report" href="/sra/docs/rca/">Root Cause Analysis: Summary and Report</a></li>
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<div class="container">
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<div class="col1">
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<h1 id="frequently-asked-questions">Frequently asked questions</h1>
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<h2 id="toc">[TOC]</h2>
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<h2 id="-ive-got-an-error-message-at-ste"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> I've got <code><an error message></code> at <code><step #></code> in the Submission Portal. How I can fix it?</h2>
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<p>Refer to the <a target="_blank" title="SRA Submission Portal Wizard Troubleshooting Guide" href="/sra/docs/submitspfiles">SRA Submission Portal Wizard Troubleshooting Guide</a> for help at every step of your submission. </p>
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<h2 id="-how-many-samples-and-experiment"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How many samples and experiments do I need?</h2>
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<p>You may have more than one experiment per sample. </p>
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<p>A <strong>Sample</strong> is a record of biological isolate with unique physical properties. </p>
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<p>Please refer to the <a target="_blank" title="SRA BioProject & BioSample Guide" href="/sra/docs/submitbio">SRA BioProject & BioSample Guide</a>
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for detailed descriptions and guidelines.</p>
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<p>An <strong>Experiment</strong> is a unique sequencing result for a specific sample. </p>
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<p>In the SRA Metadata template, Experiment is represented by a combination of <em>library + strategy + layout + instrument model</em> and corresponds to one row in the table. </p>
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<p>Please refer to the <a target="_blank" title="SRA Metadata Overview" href="/sra/docs/submitmeta">SRA Metadata Overview</a> for better understanding of
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<strong>SRA data organization</strong>. </p>
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<hr />
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<h2 id="question2gen"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> What SRA accession do I use for my publication and where can I find it?</h2>
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<p>We recommend using the BioProject accession (<strong><code>PRJNA#</code></strong>)
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in publications.</p>
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<p>A <strong>BioProject</strong> is an umbrella for all data submitted to the NCBI for a given study. Each BioProject can be associated with more than one submission in SRA. After you have successfully
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completed your submission, the SRA will send an email notification with the BioProject accession. </p>
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<hr />
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||
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||
<h2 id="question3gen"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> My manuscript reviewer is requesting a link to my submission, how do I get one?</h2>
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||
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||
<ol>
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<li>Log into the Submission Portal's <a title="Login to the Submission Portal's Manage Data" target="_blank" href="https://dataview.ncbi.nlm.nih.gov/">Manage Data</a> Interface
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</li>
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<li> Find the BioProject of interest by browsing, searching, or filtering all your data
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</li>
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<li>Press the button "Reviewer link".<br /> <br />
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</li>
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</ol>
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||
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||
<div class="shadowing">
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||
<a data-jig="ncbipopper" data-resizable="true" href="#target-3"><img src="/core/assets/sra/images/sra-updates.png" alt="Generate reviewer link for SRA data" width="500" /> </a></div>
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<div class="shadowing" id="target-3">
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<img src="/core/assets/sra/images/sra-updates.png" alt="Generate reviewer link for SRA data" width="800" /> </div>
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<p><br /> <br />
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<strong>Note</strong>: (1) The link expires after the release of the data and (2) the SRA provides access to the metadata only. </p>
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<hr />
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||
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||
<h2 id="question4gen"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> I received notification that my submission has been released. Why can't I find it in Entrez?</h2>
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||
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||
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||
<p>It may take up to 3 days for your submission to be
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||
searchable in Entrez. However, it will become public and searchable almost immediately in <a target="_blank" title="SRA Run Selector, new window" href="/Traces/study/?go=home">SRA Run Selector</a>.</p>
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<hr />
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<h2 id="-why-doesnt-my-aspera-upload-wor"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> Why doesn't my Aspera upload work?</h2>
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||
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||
<p>For troubleshooting Aspera service, please refer to <a target="_blank" title="external website, new window" href="https://support.asperasoft.com/hc/en-us">Aspera Support <img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>.</p>
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<hr />
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||
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<h2 id="question2sp"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> I registered my BioProject as well as BioSamples but I was never prompted to upload my sequence datafiles for the SRA.</h2>
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<p>To deposit your files in the SRA you need to create and finish (submit) a new submission in <a title="Submission Portal Home Page, new window" href="https://submit.ncbi.nlm.nih.gov/">the SRA Submission Portal</a>. Please refer to our <a target="_blank" title="Quick Start, new window" href="/sra/docs/submit">Quick Start</a> guide.</p>
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<hr />
|
||
|
||
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||
<h2 id="question3sp"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How do I create more than one Experiment (library/replicate) per Sample in Submission Portal?</h2>
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<p>Each row in the SRA metadata template represents one EXPERIMENT. Use the same BioSample accession or name (depending on the template) in rows (Experiments) that you want to associate with this sample.</p>
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<hr />
|
||
|
||
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<h2 id="question4sp"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How do I create more than one Run per Expermient in Submission Portal?</h2>
|
||
|
||
|
||
<p>Only one Run per Experiment is allowed in the Submission Portal. When libraries are indeed identical (same combination of <em>library + strategy + layout + instrument model</em>), all files should be placed in the same RUN. To do this simply enter the file names consecutively in the same row.</p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="question5sp"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How do I delete my submission (<strong><code>SUB#</code></strong>) in Submission Portal?</h2>
|
||
|
||
|
||
<p>To delete SRA submissions please contact SRA staff for assistance at <a href="mailto:sra@ncbi.nlm.nih.gov">sra@ncbi.nlm.nih.gov</a>. Provide <strong><code>SUB#</code></strong> and reason. To delete BioProject or BioSample submissions please contact BioProject or BioSample staff at <a href="mailto:bioprojecthelp@ncbi.nlm.nih.gov">bioprojecthelp@ncbi.nlm.nih.gov</a> and <a href="mailto:biosamplehelp@ncbi.nlm.nih.gov">biosamplehelp@ncbi.nlm.nih.gov</a> respectively Provide <strong><code>SUB#</code></strong> and reason.</p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="question6sp"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How do I add more samples to my SRA submission in Submission Portal?</h2>
|
||
|
||
|
||
<p>Submission is a discrete act of depositing data (transaction). You cannot add data to a submission. Instead, you need to add new samples and new SRA data and/or new SRA data to existing samples to a BioProject.
|
||
BioProject serves as an umbrella for all data submitted to the NCBI for a given research project. In order to update your bioproject with new samples and/or SRA data, you should create a new submission where
|
||
you provide the BioProject accession (<strong><code>PRJNA#</code></strong>) of the project you want to update. This will ensure that all pertinent data are linked to the same accession in Entrez and become searchable across databases.</p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="question7sp"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> I uploaded all data files into my personal folder, but I cannot see any files or folders when prompted to select one.</h2>
|
||
|
||
|
||
<p>Make sure that you uploaded your files into the subfolder that you created within your account folder (root directory <code>uploads/user@email.com_xyz</code>). The subfolder may not contain nested directories.
|
||
If you uploaded your files directly into your account, create a subfolder (<em><code>mkdir <name></code></em>), move your files into this directory (example of FTP command line: <code>rename fish.fastq ./data_folder/fish.fastq</code>), and allow 15 minutes for file discovery before selecting it when prompted.</p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="question1upd"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> My manuscript has been published. How do I update my SRA submission with the publication?</h2>
|
||
|
||
|
||
<p>Please refer to the <a target="_blank" title="SRA Update Guide" href="/sra/docs/submitupdate">SRA Update Guide</a></p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="-how-do-i-improvecorrect-my-meta"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How do I improve/correct my metadata after submitting?</h2>
|
||
|
||
|
||
<p>Please refer to the <a target="_blank" title="SRA Update Guide" href="/sra/docs/submitupdate">SRA Update Guide</a></p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="question3upd"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How do I withdraw my SRA Study/ExperimentT/Run in SRA (SRP#/SRX#/SRR#)?</h2>
|
||
|
||
|
||
<p>Contact the SRA staff for assistance at <a href="mailto:sra@ncbi.nlm.nih.gov">sra@ncbi.nlm.nih.gov</a>. Provide <strong><code>SRP#</code></strong>, <strong><code>SRX#</code></strong>, <strong><code>SRR#</code></strong> or your submission's ID in the form of SUB#. <br />
|
||
SRA follows INSDC policy for withdrawal and suppression requests:
|
||
<a target="_blank" title="INSDC status of documents" href="http://www.insdc.org/documents/insdc-status-document">http://www.insdc.org/documents/insdc-status-document</a> </p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="-how-do-i-rename-my-experiementr"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How do I re-name my Experiement/Run?</h2>
|
||
|
||
|
||
<p>Aliases of Experiments and Runs cannot be changed.
|
||
They are used for internal tracking only, which means that they will not be visible to the public during normal usage of the database. However, you
|
||
always can improve the <strong>Title</strong> of the Experiment by logging in <a title="Manage Data" href="https://dataview.ncbi.nlm.nih.gov/?archive=bioproject">the SRA Submission Portal</a>
|
||
directly, editing text in the Experiment's field <strong>Title</strong> and clicking the button <strong>Save</strong>. </p>
|
||
|
||
|
||
<p>See <a title="Updating SRA data, new window" href="/sra/docs/submitupdate">Updating SRA data</a> help page for more information.</p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="-how-do-i-change-the-platform-in"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How do I change the PLATFORM in my Experiements?</h2>
|
||
|
||
|
||
<p>Contact SRA staff for assistance at <a href="mailto:sra@ncbi.nlm.nih.gov?subject=Need%20to%20change%20Platform&body=Dear%20SRA%20staff">sra@ncbi.nlm.nih.gov</a></p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="-how-do-i-link-an-experiement-to"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How do I link an Experiement to a different Sample?</h2>
|
||
|
||
|
||
<p>1) Log into <a title="Manage Data" href="https://dataview.ncbi.nlm.nih.gov/?archive=bioproject">the SRA Submission Portal</a></p>
|
||
|
||
|
||
<p>2) From the bottom of the <em>BioProject</em> page, <strong>select the runs</strong> you want to update</p>
|
||
|
||
|
||
<p>3) Click the <strong>Edit metadata</strong> button</p>
|
||
|
||
|
||
<p>4) Change the values in the biosample accession field</p>
|
||
|
||
|
||
<p>5) Click the <strong>Submit</strong> button</p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="-how-do-i-link-a-run-to-a-differ"><img src="/core/assets/sra/images/Question.png" alt="Question" width="20" /> How do I link a RUN to a different Experiement?</h2>
|
||
|
||
|
||
<p>Contact SRA staff for assistance
|
||
at <a href="mailto:sra@ncbi.nlm.nih.gov">sra@ncbi.nlm.nih.gov</a>.</p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="contact-sra">Contact SRA</h2>
|
||
|
||
|
||
<p>If you were unable to resolve your problem after reading this guide, contact SRA staff at <a href="mailto:sra@ncbi.nlm.nih.gov">sra@ncbi.nlm.nih.gov</a>.</p>
|
||
|
||
|
||
<ul>
|
||
<li>Include all pertinent identifiers (**`SUB#`**, **`PRJNA#`**, **`SRP#`**, **`SRX#`**, **`SRR#`**, etc.) and state your problem clearly.</li>
|
||
<li>Do not create duplicate submissions</li>
|
||
</ul>
|
||
|
||
|
||
</div>
|
||
<!--/.col1-->
|
||
<div class="col2">
|
||
<div id="shared-content-1">
|
||
<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>
|
||
</ul>
|
||
<h2 data-heading="h2" data-no-toc="true">Submitting Data to SRA</h2>
|
||
<h3 class="nav" data-heading="h3" data-no-toc="true">General</h3>
|
||
<ul>
|
||
<li><a title="SRA Submission Quick Start" href="/sra/docs/submit">Quick Start</a></li>
|
||
<li><a title="How to submit BioProject and BioSample for SRA" href="/sra/docs/submitbio">BioProject & BioSample</a></li>
|
||
<li><a title="SRA file format guide" href="/sra/docs/submitformats">File Format Guide</a></li>
|
||
<li><a title="Understanding SRA Metadata and Submission Overview" href="/sra/docs/submitmeta">SRA Metadata Overview</a></li>
|
||
<li><a title="SRA File Upload" href="/sra/docs/submitfiles">SRA File Upload</a></li>
|
||
<li><a title="SRA Frequently Asked Questions" href="/sra/docs/submitquestions">Frequently Asked Questions</a></li>
|
||
</ul>
|
||
<h3 class="nav" data-heading="h3" data-no-toc="true">SRA Submission Portal</h3>
|
||
<ul>
|
||
<li><a title="Submitting Data in Submission Portal" href="/sra/docs/submitportal">Submitting to SRA</a></li>
|
||
<li><a title="Troubleshooting SRA submission" href="/sra/docs/submitspfiles">Troubleshooting Submission</a></li>
|
||
</ul>
|
||
<h3 class="nav" data-heading="h3" data-no-toc="true">Submitting for dbGaP & GEO</h3>
|
||
<ul>
|
||
<li><a title="Submitting SRA data for dbGaP project" href="/sra/docs/submitdbgap">Submitting for dbGaP</a></li>
|
||
<li><a title="Submitting SRA data for GEO" href="/sra/docs/submitgeo">Submitting for GEO</a></li>
|
||
</ul>
|
||
<h3 class="nav" data-heading="h3" data-no-toc="true">Updating SRA Data</h3>
|
||
<ul>
|
||
<li><a title="Updating SRA submission" href="/sra/docs/submitupdate">Updating SRA data</a> </li>
|
||
<li><a title="Request status change" href="/sra/docs/request-status-change">Request status change</a> </li>
|
||
<li><a title="Change release date" href="/sra/docs/submitsra">Change Release Date</a></li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
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