Update CDS_access.md

Added CDS screenshots
ncihtan · Oct 12, 2023 · 0365110 · 0365110
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 # NCI's Cancer Data Service
 
-The [CDS Portal](https://dataservice.datacommons.cancer.gov/), within NCI's Cancer Research Data Commons (CRDC), provides access to both open and controlled access data. 
+The [CDS Portal](https://dataservice.datacommons.cancer.gov/), 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). 
 
-CDS currently hosts a variety of data types from NCI projects, including those from the [Human Tumor Atlas Network](https://dataservice.datacommons.cancer.gov/#/study/phs002371). 
+In order to access these HTAN data within the [CDS Portal](https://dataservice.datacommons.cancer.gov/), navigate to the portal in a web browser and click on the **Explore CDS Data** button on the landing page.
+
+<p align="center"><img width="364" alt="1" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/40aff1af-a58f-49dc-9253-6ee5e67ef419">
+</p>
+
+&nbsp;
+
+On the Data Explorer page, expand the STUDY section on the left sidebar, scroll down, and check the box next to **Human Tumor Atlas (HTAN) primary sequence data**.
+
+<p align="center"><img width="891" alt="Figure 2" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/4a3b97f6-97d6-4c99-b782-88c9a8a74fba"></p>
+
+&nbsp;
+
+This action will change the summary panel to reflect selecting HTAN data only.
+
+<p align="center"><img width="891" alt="Figure 3" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/14e07c72-16d4-463a-b8b2-1ef5f8d72107"></p>
+
+&nbsp;
+
+Scroll down, or click on the **Collapse View** tab on the upper right just below the query summary line in order to see the tabulated view of all of the participants, samples or files in HTAN.
+
+<p align="center"><img width="891" alt="Figure 4" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/87e90271-a525-4ff7-baeb-4c75ea073a91"></p>
+
+&nbsp;
+
+Click on the **Add All Files** button, or select the check boxes next to all Participants, Samples or Files for a subselection and then click on the **Add Selected** button.  This action will update your cart icon in the upper right corner.
+
+<p align="center"><img width="891" alt="Figure 5" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/e79dd76d-8eb1-460f-8957-0e07b3898845"></p>
+
+&nbsp;
+
+Clicking on the cart icon, will bring up a list of the selected files.  Click on the **Download Manifest** button in the upper right to download a CSV-formated (Excel compatible) file of this file list.
+
+<p align="center"><img width="891" alt="Figure 6" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/d3addd28-652d-4320-a109-d0080d1d37df"></p>
+
+&nbsp;
+
+Once this file manifest is downloaded, it will have to be uploaded into your [Seven Bridges Cancer Genomics Cloud](https://www.cancergenomicscloud.org/) account, in order for you to be able to download, or otherwise compute on, these data.  **NOTE**: dbGaP approval for HTAN study [phs002371](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002371.v3.p1) is required in order to access HTAN lower-level genomics data, such as RNAseq FASTQ and BAM files.
 
-dbGaP approval for HTAN study [phs002371](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002371.v3.p1) is required in order to access HTAN lower-level genomics data, such as RNAseq FASTQ and BAM files.