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Merge pull request #22 from ncihtan/specific_assay_files
- information about entityIDs, prepopulating manifests. - additional of assay specifc docs for biospecimen, clinical, RPPA. - chgs to CDS/CGC data access.
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| <title>cds_access</title> | ||
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| <script src="CDS_access_files/libs/clipboard/clipboard.min.js"></script> | ||
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| <section id="accessing-sequence-data-via-ncis-cancer-data-service-cds" class="level1"> | ||
| <h1>Accessing Sequence Data via NCI’s Cancer Data Service (CDS)</h1> | ||
| <p>!!! <strong>NOTE</strong>: dbGaP approval for HTAN study <a href="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002371.v3.p1">phs002371</a> is required in order to access HTAN lower-level genomics data, such as RNAseq FASTQ and BAM files. !!!</p> | ||
| <p>The <a href="https://dataservice.datacommons.cancer.gov/">CDS Portal</a>, within NCI’s Cancer Research Data Commons (CRDC), provides an interface to filter and select data from a variety of NCI programs, including controlled-access, primary sequence data from the Human Tumor Atlas Network (HTAN). This page provides directions for importing sequencing data from CDS to the <a href="https://cancergenomicscloud.org/">Cancer Genomics Commons (CGC)</a>.</p> | ||
| <p>The directions for accessing sequencing data on CDS are similar to those for <a href="../open_access/cds_imaging.md">Level 2 Imaging Data Access</a>, including Direct Export from CDS to CGC and importing data using a Data Repository Service (DRS) Manifest. Please follow the <a href="../open_access/cds_imaging.md">Level 2 Imaging Data Access</a> directions to access sequencing data, noting the following changes:</p> | ||
| <ol type="1"> | ||
| <li>For Direct Export or Generating a DRS Manifest from CDS, choose <strong>Human Tumor Atlas (HTAN) primary sequence data</strong> on the STUDY section of the left hand sidebar instead of <strong>Human Tumor Atlas (HTAN) imaging data</strong>.</li> | ||
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| <img width="891" alt="Figure 3" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/14e07c72-16d4-463a-b8b2-1ef5f8d72107"> | ||
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| <p> </p> | ||
| <ol start="2" type="1"> | ||
| <li>To generate a DRS Manifest from the <a href="https://humantumoratlas.org/">HTAN Data Portal</a>, click <strong>CDS/SB-CGC (dbGaP)</strong> under the <strong>Data Access</strong> filter instead of <strong>CDS/SB-CGC (Open Access)</strong>.</li> | ||
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| <p><img src="../img/cds_genomics1.png" class="img-fluid figure-img"></p> | ||
| <figcaption class="figure-caption">HTAN Portal: Accessing Genomic Data in CDS</figcaption> | ||
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