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550 lines
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<h1 id="access-trace-data">Access Trace Data</h1>
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<div class="jig-ncbiinpagenav" data-all-heading-levels="["h2"]" data-top-of-page-t-o-c="true">
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<h2 id="introduction">Introduction</h2>
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<div class="warning-message"> <img src="/core/assets/sra/images/tack.png" alt="Tack" height="20" /> As a result of diminished usage and aging hardware
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infrastructure, <strong>the Trace Archive</strong>, which previously stored capillary sequence data submitted to NCBI, has been retired.
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</div>
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<p>Capillary sequence data may still be submitted to the NCBI <a title="Sequence Read Archive" href="/sra/">Sequence Read Archive (SRA)</a> via
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<a title="SRA Submission Portal" href="https://submit.ncbi.nlm.nih.gov/subs/sra/">Submission Portal</a>. <br />
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All data previously stored in the <strong>Trace Archive</strong> has been transferred to SRA and may be found in Entrez using standard search terms or accessed directly by <strong>TI</strong> number. </p>
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<h2 id="searching-for-trace-archive-data">Searching for Trace Archive data in Sequence Read Archive (SRA) Entrez</h2>
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<p>Trace data can be searched in Entrez and accessed like any other data housed in SRA. Users may search by Organism,
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Center Name, or other metadata terms in SRA Entrez. The key distinction in Entrez is that after entering a search, users should ensure the <strong>Capillary</strong> option is selected from the
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<strong>Platform</strong> section of the facet list on the left side of the results page. </p>
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<h3 id="examples">Examples</h3>
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<p>Go to <a title="Sequence Read Archive" href="/sra/">SRA Home page</a> and </p>
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<h4 id="find-all-capillary-sequencing-re">Find all capillary sequencing records</h4>
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<p>Type in the search box <a target="_blank" title="search by platform, new window" href="/sra?term=%22platform%20capillary%22%5BProperties%5D">"platform capillary"[Properties]</a> </p>
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<h4 id="find-capillary-records-for-term-">Find capillary records for term 'cancer'</h4>
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<ol>
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<li>Type "cancer" in the search field: <a target="_blank" title="search for cancer in SRA, new window" href="/sra/?term=cancer">cancer</a> </li>
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<li>Click "Capillary" in <strong>Platform</strong> section of the facet list on the left side of the results page </li>
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</ol>
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<h2 id="accessing-trace-archive-data-fro">Accessing Trace Archive data from SRA Entrez</h2>
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<h3 id="run-browser">Run Browser</h3>
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<p>If interested in a few specific records, users can click on individual entries from the Entrez results page
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to see a more detailed breakdown of the record metadata. From there users may click on a Run accession link in the 'Runs' section to see
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the record in <a target="_blank" title="Run Browser, new window" href="/Traces/sra/sra.cgi?view=run_browser">Run Browser <img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>
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where individual reads can be viewed and the data can be downloaded manually in SRA normalized format.</p>
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<h4 id="example">Example</h4>
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<p><a target="_blank" title="Run Browser, new window" href="/Traces/sra/?run=SRR19207298">/Traces/sra/?run=SRR19207298 <img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a> </p>
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<h3 id="run-selector">Run Selector</h3>
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<p>Users preferring to look at and further refine a larger set of records can send the Entrez results to the <strong>Run Selector</strong>: </p>
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<ul>
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<li>Click <strong>Send to</strong> on the top of the results page, check the <strong>Run Selector</strong> radiobutton, and click the button <strong>Go</strong>. </li>
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<li>If necessary, refine your results by using various filters provided by the <strong>Run Selector</strong>'s interface.</li>
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<li>Click the <strong>Metadata</strong> button. This will generate a tabular <code>SraRunTable.txt</code> file with metadata available for each Run. </li>
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</ul>
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<h4 id="example_1">Example</h4>
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<p><a target="_blank" title="Run Browser, new window" href="/Traces/study/?uids=21811665%2C21799678%2C21799677&o=acc_s%3Aa">Three selected runs in the Run Selector <img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a> </p>
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<h2 id="downloading-trace-archive-data-u">Downloading Trace Archive data using SRA Toolkit</h2>
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<p>Once a user has one or more Run accessions of interest, the SRA Toolkit can be used to access the data in <code>fasta</code> or <code>fastq</code> format like
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<a target="_blank" title="SRA Download Guide, new window" href="/sra/docs/sradownload/">any other SRA data</a>.
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For example, <code>fasta</code> data can be obtained from any Run accessions with a toolkit command like:</p>
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<p><code>fasterq-dump --fasta SRR9495649</code> </p>
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<p>For more information on installing and using the SRA Toolkit to access these data, please see </p>
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<ul>
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<li><a target="_blank" title="SRA Download Guide, new window" href="/sra/docs/sradownload/">SRA Download Guide</a> or </li>
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<li><a target="_blank" title="GitHub, new window" href="https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit">GitHub page <img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a> </li>
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</ul>
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<h2 id="accessing-trace-archive-data-by-">Accessing Trace Archive data by TI Number</h2>
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<p>For users that want to access specific Trace Archive records by <strong>TI</strong> number, SRA provides a service to access these data directly in <code>fasta</code> format that can
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be called from the command line. This web service can process one or more TI numbers simultaneously using a comma delimited list (eg: TI numbers 10, 20, and 30): </p>
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<p><code>curl "https://www.ncbi.nlm.nih.gov/Traces/sra-reads-be/fasta?ti=10,20,30&retmode=text"</code> </p>
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<p>You can use <code>retmode=raw</code> or remove the <code>retmode</code> element entirely to access the data in <code>.gz</code> format: </p>
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<p><code>curl "https://www.ncbi.nlm.nih.gov/Traces/sra-reads-be/fasta?ti=10,20,30&retmode=raw" > output_fasta.gz</code> </p>
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<p>If the list includes any invalid TI numbers, an error will be returned: "Unrecognized TIs were found".
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To have the service ignore bad TI numbers ('badTI' below) and return fasta records for all valid TIs in the request, add the <code>ignore_bad_tis</code> parameter: </p>
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<p><code>curl "https://www.ncbi.nlm.nih.gov/Traces/sra-reads-be/fasta?ti=10,20,badTI&ignore_bad_tis&retmode=text"</code> </p>
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<p>While there is no limit to the number of TIs that can be queried per request, using the syntax above can lead to an error if the length of
|
|
the URL is too large: "414 Request-URI Too Long". To query a set of TIs that exceeds this length, please create a text file containing the
|
|
TI numbers in a single, comma-delimited line, e.g.: </p>
|
|
<p><code>100001,100002,100003,100004,100005</code></p>
|
|
<p>To download the data in a gzipped fasta file for a list of TIs in a file named 'ti.txt'
|
|
in the current working directory, the curl command is: </p>
|
|
<p><code>curl -F "ti=@./ti.txt" 'https://www.ncbi.nlm.nih.gov/Traces/sra-reads-be/fasta?retmode=raw&ignore_bad_tis=1' > ti.fasta.gz</code> </p>
|
|
<h2 id="legacy-support-for-query_tracedb">Legacy Support for <code>query_tracedb</code></h2>
|
|
<p>In the past the <strong>query_tracedb</strong> script could be used to access Trace Archive data by TI number,
|
|
and this will continue to function as all queries via this old method will be redirected to our new service
|
|
automatically. The fasta output format will remain the same, ensuring that existing scripts or pipelines that use the
|
|
<strong>query_tracedb</strong> tool should continue to function normally. However, features of the <strong>query_tracedb</strong> script other than <code>fasta</code> retrieval by
|
|
TI number will no longer
|
|
function or be supported and we recommend that users migrate to using the new service mentioned above as soon as possible. </p>
|
|
<hr />
|
|
<h2 id="contact-sra">Contact SRA</h2>
|
|
<p>Contact SRA staff for assistance at <a href="mailto:sra@ncbi.nlm.nih.gov?subject=SRA%20question&body=Dear%20SRA%20staff">sra@ncbi.nlm.nih.gov</a> </p>
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</div>
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<h2 data-heading="h2" data-no-toc="true">Getting Started</h2>
|
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<ul>
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<li><a title="SRA Getting Started" href="/sra/docs/">Getting Started</a></li>
|
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</ul>
|
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<h2 data-heading="h2" data-no-toc="true">Downloading SRA Data</h2>
|
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<ul>
|
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<li><a title="Download SRA sequences from Entrez search results" href="/sra/docs/sradownload">Download Guide</a> </li>
|
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<li><a title="dbGAP Download Guide" href="/sra/docs/sra-dbgap-download">dbGaP Download Guide</a> </li>
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<li><a title="Data Delivery to cloud bucket" href="/sra/docs/data-delivery">Data Delivery to Cloud</a> </li>
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<li><a title="Access Trace Data" href="/sra/docs/trace-data">Access Trace Data</a> </li>
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</ul>
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<h2 data-heading="h2" data-no-toc="true">Search SRA</h2>
|
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<ul>
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<li><a title="Search in SRA" href="/sra/docs/srasearch">Search in SRA Entrez</a> </li>
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<li><a title="SRA cloud-based search" href="/sra/docs/sra-cloud-based-examples">Cloud-based Search</a> </li>
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<li><a title="SRA in BigQuery" href="/sra/docs/sra-bigquery-examples">Search in BigQuery</a> </li>
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<li><a title="SRA in Athena" href="/sra/docs/sra-athena-examples">Search in Athena</a> </li>
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</ul>
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<h2 data-heading="h2" data-no-toc="true">Browsing</h2>
|
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<ul>
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<li><a target="_blank" title="SRA Run Selector" href="/Traces/study/">SRA Run Selector</a> </li>
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<li><a target="_blank" title="Browse Samples, new window" href="/Traces/sra/sra.cgi?view=samples">Samples</a> </li>
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<li><a target="_blank" title="Browse Analyses, new window" href="/Traces/sra/sra.cgi?view=analysis">Analyses</a> </li>
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<li><a target="_blank" title="Run Browser" href="/Traces/sra/sra.cgi?view=run_browser">Data for a single RUN</a> </li>
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</ul>
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<h2 data-heading="h2" data-no-toc="true">SRA-BLAST</h2>
|
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<li><a target="_blank" title="SRA Blast Step by Step" href="https://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_LocalSRABlast_StepByStep.pdf">SRA BLAST How To</a> </li>
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</ul>
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<h3 id="use-cases">Use cases</h3>
|
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<ul>
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<li><a target="_blank" title="The Tasmanian Devil and Cancer as an Infectious Disease: Analysis of transcriptome data, new window" href="https://ncbiinsights.ncbi.nlm.nih.gov/2013/02/27/the-tasmanian-devil-and-cancer-as-an-infectious-disease-analysis-of-transcriptome-data/">Transcriptome analysis<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a></li>
|
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<li><a target="_blank" title="Exploring next-gen sequencing experiments with SRA-BLAST, new window" href="/books/NBK431007/">Metagenome analysis<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a></li>
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