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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>GaP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2009-. </p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/helpdbgap/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-helpdbgap-lrg.png" alt="Cover of GaP FAQ Archive" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>GaP FAQ Archive [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK570250_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK570250_dtls__"><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>; 2009-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/helpdbgap/">Contents</a></li></ul></div><div class="bk_noprnt"><form method="get" action="/books/n/helpdbgap/" id="bk_srch"><div class="bk_search"><label for="bk_term" class="offscreen_noflow">Search term</label><input type="text" title="Search this book" id="bk_term" name="term" value="" data-jig="ncbiclearbutton" /> <input type="submit" class="jig-ncbibutton" value="Search this book" submit="false" style="padding: 0.1em 0.4em;" /></div></form></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpdbgap/Dwnld_DownloadData/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/helpdbgap/Dwnld_DataSample/" title="Next page in this title">Next ></a></div></div></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK570250_"><span class="title" itemprop="name">Decrypting and Extracting Data</span></h1><p class="small">Created: <span itemprop="datePublished">October 22, 2008</span>; Last Update: <span itemprop="dateModified">August 12, 2013</span>.</p><p><em>Estimated reading time: 2 minutes</em></p></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><ul class="simple-list"><li><h4>File Decryption</h4></li><li><p><a href="#Dwnld_DecryptExtrct.are_downloaded_files">Are downloaded files encrypted? If so, do I need to decrypt them and how?</a></p></li></ul><ul class="simple-list"><li><h4>SRA to BAM format conversion</h4></li><li><p><a href="#Dwnld_DecryptExtrct.we_would_like_to_get">We would like to get the data in BAM format but they are only available in SRA format. What can we do?</a></p></li></ul><ul class="simple-list"><li><h4>SRA fastq-dump Utility</h4></li><li><p><a href="#Dwnld_DecryptExtrct.how_to_convert_downl">How to convert downloaded SRA data into FASTQ format?</a></p></li></ul><div id="Dwnld_DecryptExtrct.File_Decryption"><h2 id="_Dwnld_DecryptExtrct_File_Decryption_">File Decryption</h2><div><h4 id="Dwnld_DecryptExtrct.are_downloaded_files">Are downloaded files encrypted? If so, do I need to decrypt them and how?</h4><blockquote><p>The following instructions are nearly identical in all supported platforms.</p><dl class="temp-labeled-list"><dt>1.</dt><dd><p class="no_top_margin">
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<b>Different treatment of SRA and non-SRA data</b>
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</p><p>The data files distributed through the dbGaP are all encrypted by NCBI’s data encryption algorithm. These files have a file suffix “.ncbi_enc”, indicating that they are NCBI encrypted files. Not all encrypted data however need to be decrypted.</p><p>The SRA (short-read-archive) data distributed through the dbGaP are encrypted <b>but there is no need to decrypt them</b>. The NCBI SRA toolkit can work directly on encrypted SRA data without decryption. Decrypted SRA data is in a binary format that is not human readable and can only be processed by the SRA toolkit anyway.</p><p>You need NCBI SRA toolkit to work on SRA data. The SRA toolkit is a collection of utilities that can dump, extract, and convert SRA data to different data formats. The vdb-decrypt utility included in the SRA toolkit can be used to decrypt any encrypted dbGaP data.</p><p>The dbGaP data other than SRA (non-SRA data) need to be decrypted before use. If you are only working on non-SRA data, you can download the NCBI Decryption Tool, which is a sub-set of the SRA Toolkit. It only includes utilities related to data decryption. If you already have SRA toolkit setup, you don’t need to download NCBI decryption tool because the vdb-decrypt utility is included.</p><p>Both NCBI SRA Toolkit and NCBI Decryption Tool are available from <a href="/Traces/sra/?view=software" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">here</a>.</p></dd><dt>2.</dt><dd><p class="no_top_margin">
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<b>The dbGaP repository key</b>
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</p><p>dbGaP repository key is a dbGaP project wide security token required for configuring NCBI SRA toolkit and decryption tools. The key is provided in a file with suffix “.ngc”. It can be obtained from two places in PI’s dbGaP account.</p><dl class="temp-labeled-list"><dt>1.</dt><dd><p class="no_top_margin">The first place is the project page under “My Projects” tab, through a link named “get dbGaP repository key” in the “Actions” column. The key downloaded from here is valid to all downloaded data under the project.</p></dd><dt>2.</dt><dd><p class="no_top_margin">The second place is the download page under “Downloads” tab, through a link named “get dbGaP repository key in the “Actions” column.</p></dd></dl></dd><dt>3.</dt><dd><p class="no_top_margin">
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<b>Toolkit Configuration and import repository key</b>
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</p><p>The NCBI decryption tool is a subset of the SRA Toolkit. The steps of setting up both tools are nearly identical. In either case, a dbGaP repository key for the respective dbGaP project should be downloaded from PI’s dbGaP account, and the tool should be first configured using “vdb-config”, a command line utility available under the “bin” directory of the toolkit. See <a href="/Traces/sra/sra.cgi?view=toolkit_doc&f=std" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">here</a> for detailed instruction.</p></dd><dt>4.</dt><dd><p class="no_top_margin">
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<b>Decrypting Non-SRA Data</b>
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</p><p>The Non-SRA data distributed through the dbGaP need to be decrypted before used for anything. The tool named “vdb-decrypt” under NCBI sra-toolkit or NCBI decryption Tools is for data decryption.</p><p>To decrypt non-SRA data, go to the dbGaP project directory (workspace) setup through the toolkit configuration, issue the following command from a command line: It is important to remember that the command line has to be run directly from the dbGaP project directory.</p><p>A typical vdb-decrypt command should be like this: <br /><i>$ /path-to-your-sratoolkit-installation-dir/bin/vdb-decrypt --ngc /path-to-ngc-file-dir/xxxxx.ngc /path-to-top-level-download-dir/</i></p></dd><dt>5.</dt><dd><p class="no_top_margin">
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<b>More about NCBI SRA Toolkit</b>
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</p><p>Please refer to the <a href="/Traces/sra/sra.cgi?view=toolkit_doc" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">documentation of sra-toolkit</a> for more about various utilities available under the sra-toolkit.</p></dd></dl><p>(<b>12/09/2020</b>)</p></blockquote></div></div><div id="Dwnld_DecryptExtrct.SRA_to_BAM_format_co"><h2 id="_Dwnld_DecryptExtrct_SRA_to_BAM_format_co_">SRA to BAM format conversion</h2><div><h4 id="Dwnld_DecryptExtrct.we_would_like_to_get">We would like to get the data in BAM format but they are only available in SRA format. What can we do?</h4><blockquote><p>Most of the sequencing data available through the dbGaP are in SRA format. The SRA data can be converted to BAM format using the sam-dump combined with samtools. The sam-dump utility is available under the SRA toolkit. More information about the sam-dump is available at <a href="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=sam-dump" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">here</a>, and the information about the samtools can be found from <a href="http://www.htslib.org/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">here</a>.</p><p>(<b>12/24/2013</b>)</p></blockquote></div></div><div id="Dwnld_DecryptExtrct.SRA_fastqdump_Utilit"><h2 id="_Dwnld_DecryptExtrct_SRA_fastqdump_Utilit_">SRA fastq-dump Utility</h2><div><h4 id="Dwnld_DecryptExtrct.how_to_convert_downl">How to convert downloaded SRA data into FASTQ format?</h4><blockquote><p>Please visit the section related to the fastq-dump utility in <a href="/books/NBK47540/#SRA_Download_Guid_B.3_Installing_the_Tool" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">SRA Download Guide</a>. If you have further questions regarding SRA (Short-Read-Archive) data, please directly contact NCBI’s SRA group (<a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@ars" class="oemail">vog.hin.mln.ibcn@ars</a>). They are better able to help with SRA related issues.</p><p>(<b>10/19/2011</b>)</p></blockquote></div></div><div id="bk_toc_contnr"></div></div></div>
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<div class="post-content"><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div><div class="small"><span class="label">Bookshelf ID: NBK570250</span></div><div style="margin-top:2em" class="bk_noprnt"><a class="bk_cntns" href="/books/n/helpdbgap/">Contents</a><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpdbgap/Dwnld_DownloadData/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/helpdbgap/Dwnld_DataSample/" title="Next page in this title">Next ></a></div></div></div></div>
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<div xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"></div><div class="portlet"><div class="portlet_head"><div class="portlet_title"><h3><span>Views</span></h3></div><a name="Shutter" sid="1" href="#" class="portlet_shutter" title="Show/hide content" remembercollapsed="true" pgsec_name="PDF_download" id="Shutter"></a></div><div class="portlet_content"><ul xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" class="simple-list"><li><a href="/books/NBK570250/?report=reader">PubReader</a></li><li><a href="/books/NBK570250/?report=printable">Print View</a></li><li><a data-jig="ncbidialog" href="#_ncbi_dlg_citbx_NBK570250" data-jigconfig="width:400,modal:true">Cite this Page</a><div id="_ncbi_dlg_citbx_NBK570250" style="display:none" title="Cite this Page"><div class="bk_tt">GaP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2009-. Decrypting and Extracting Data. 2008 Oct 22 [Updated 2013 Aug 12].<span class="bk_cite_avail"></span></div></div></li><li><a href="/books/NBK570250/pdf/Bookshelf_NBK570250.pdf">PDF version of this page</a> (76K)</li><li><a href="/books/n/helpdbgap/pdf/">PDF version of this title</a> (1.7M)</li></ul></div></div><div class="portlet"><div class="portlet_head"><div class="portlet_title"><h3><span>In this Page</span></h3></div><a name="Shutter" sid="1" href="#" class="portlet_shutter" title="Show/hide content" remembercollapsed="true" pgsec_name="page-toc" id="Shutter"></a></div><div class="portlet_content"><ul xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" class="simple-list"><li><a href="#Dwnld_DecryptExtrct.File_Decryption" ref="log$=inpage&link_id=inpage">File Decryption</a></li><li><a href="#Dwnld_DecryptExtrct.SRA_to_BAM_format_co" ref="log$=inpage&link_id=inpage">SRA to BAM format conversion</a></li><li><a href="#Dwnld_DecryptExtrct.SRA_fastqdump_Utilit" ref="log$=inpage&link_id=inpage">SRA fastq-dump Utility</a></li></ul></div></div><div class="portlet"><div class="portlet_head"><div class="portlet_title"><h3><span>Other titles in this collection</span></h3></div><a name="Shutter" sid="1" href="#" class="portlet_shutter" title="Show/hide content" remembercollapsed="true" pgsec_name="source-links" id="Shutter"></a></div><div class="portlet_content"><ul xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" class="simple-list"><li><a href="/books/n/helpcollect/">NCBI Help Manual</a></li></ul></div></div><div class="portlet"><div class="portlet_head"><div class="portlet_title"><h3><span>Recent Activity</span></h3></div><a name="Shutter" sid="1" href="#" class="portlet_shutter" title="Show/hide content" remembercollapsed="true" pgsec_name="recent_activity" id="Shutter"></a></div><div class="portlet_content"><div xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="HTDisplay" class=""><div class="action"><a href="javascript:historyDisplayState('ClearHT')">Clear</a><a href="javascript:historyDisplayState('HTOff')" class="HTOn">Turn Off</a><a href="javascript:historyDisplayState('HTOn')" class="HTOff">Turn On</a></div><ul id="activity"><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=1" href="/portal/utils/pageresolver.fcgi?recordid=67c8157cd5edb449bfc001a2">Decrypting and Extracting Data - GaP FAQ Archive</a><div class="ralinkpop offscreen_noflow">Decrypting and Extracting Data - GaP FAQ Archive<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=2" href="/portal/utils/pageresolver.fcgi?recordid=67c8157bfeee5b00ac7b6221">Starting Point to Applying for dbGaP Data - GaP FAQ Archive</a><div class="ralinkpop offscreen_noflow">Starting Point to Applying for dbGaP Data - GaP FAQ Archive<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=3" href="/portal/utils/pageresolver.fcgi?recordid=67c8157ad5edb449bfbfea24">Data Access Requests - GaP FAQ Archive</a><div class="ralinkpop offscreen_noflow">Data Access Requests - GaP FAQ Archive<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=4" href="/portal/utils/pageresolver.fcgi?recordid=67c81578b70fbb1960831be2">Aspera Transfer Guide - SRA Handbook</a><div class="ralinkpop offscreen_noflow">Aspera Transfer Guide - SRA Handbook<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=5" href="/portal/utils/pageresolver.fcgi?recordid=67c81576feee5b00ac7b372b">Understanding SRA Search Results - SRA Knowledge Base</a><div class="ralinkpop offscreen_noflow">Understanding SRA Search Results - SRA Knowledge Base<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li></ul><p class="HTOn">Your browsing activity is empty.</p><p class="HTOff">Activity recording is turned off.</p><p id="turnOn" class="HTOff"><a href="javascript:historyDisplayState('HTOn')">Turn recording back on</a></p><a class="seemore" href="/sites/myncbi/recentactivity">See more...</a></div></div></div>
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