Search files on the CGC

You can quickly locate files in a project or among Public Reference Files via keyword searching or metadata filtering. You can browse TCGA repository using [the Case Explorer](doc:the-case-explorer) or [the Data Browser](doc:the-data-browser). Once you copy TCGA files to a project, you can follow the steps below to quickly locate them. [block:callout] { "type": "warning", "title": "On this page:", "body": "* [Keyword search](#section-keyword-search)\n* [Filter by metadata fields](#section-filter-by-metadata-fields)\n* [Sort by metadata fields](#section-sort-by-metadata-fields)" } [/block] ##Keyword search You can use the search bar at the top of each file repository to find files by entering the file name or notes associated with a file. In the example below, searching for **1000g** in the **Public Reference Files** repository filters for all the files that have **1000g** in their names or in their associated notes. [block:image] { "images": [ { "image": [ "https://files.readme.io/JEN1WYRwTDSRsG4dGOsW_filter%20files.jpg", "filter files.jpg", "1883", "715", "#0f58a5", "" ], "caption": "Keyword search", "border": true } ] } [/block] Click the loupe icon to choose whether the search will only be applied to the current folder or it should also include subfolders. [block:image] { "images": [ { "image": [ "https://files.readme.io/9a2e202-search-files-on-platform-cgc.jpg", "search-files-on-platform-cgc.jpg", 687, 343, "#e3eaee" ] } ] } [/block] ##Filter by metadata fields Once you have [set your files' metadata](doc:metadata-for-private-data), you can use this information to filter files. Next to the search bar in each repository are drop-down menus for the metadata fields **File extension**, **Sample ID**, and **Task** (see below). Selecting a particular metadata value from one of these menus displays only files that match the value. You can add additional drop-down menus to filter by other metadata fields by clicking the **+** icon. [block:image] { "images": [ { "image": [ "https://files.readme.io/Bb6wI8RhQE2a1AJMlUIC_filter%20cgc.jpg", "filter cgc.jpg", "1617", "715", "#1258a2", "" ], "caption": "Filter by metadata fields" } ] } [/block] <div align="right"><a href="#top">top</a></div> ##Sort by metadata fields You can sort files in a project based on the metadata associated with them. The **Files** tab displays each file and its metadata value in your project in a table format. You can add more metadata fields, including custom metadata fields, by clicking the gear table and selecting the metadata field(s). Hovering over the name of a metadata field brings up the sort icon <img src="https://files.readme.io/wNx2UI9GTF2G06FK8SMn_sort-icon.png" height="20px" width="auto" align="inline" style="margin:1px"/>. Clicking this icon arranges files by their values for the chosen metadata field. [block:image] { "images": [ { "image": [ "https://files.readme.io/1dc5dcd-Screen_Shot_2016-12-15_at_11.29.20_AM.png", "Screen Shot 2016-12-15 at 11.29.20 AM.png", 708, 537, "#f6f6f5" ], "caption": "Sort by metadata fields", "border": true } ] } [/block] ##Filter by tags Public reference files on the Seven Bridges Platform are labeled with tags which you can use as a criteria for filtering. To start filtering by tags, click the Tags drop-down and select a tag (e.g. WGS). The list of files will be refreshed based on on your choice. [block:image] { "images": [ { "image": [ "https://files.readme.io/34e3a08-cgc-filter-by-tags.png", "cgc-filter-by-tags.png", 746, 607, "#e8ebeb" ], "border": true } ] } [/block] You can use multiple tags as a criteria by selecting more than one tag. In addition, you can use the search box just below the drop-down menu to look for specific tags. [block:callout] { "type": "info", "body": "The tag(s) which are currently applied as a filter will be highlighted in the list of files" } [/block] For further information about tags on public files and their meaning, please see the table below: [block:parameters] { "data": { "h-0": "Tag", "h-1": "Description", "0-0": "WGS", "0-1": "Whole genome sequencing", "1-0": "WES", "1-1": "Whole exome sequencing", "2-0": "Index", "2-1": "Index files", "3-0": "Tumor sample", "3-1": "Files from the tumor sample", "4-0": "Normal sample", "4-1": "Files from the normal sample", "5-0": "Reference build v37", "5-1": "Files compatible with human reference genome hg19/GRCh37", "6-0": "Reference build v38", "6-1": "Files compatible with human reference genome hg38/GRCh38", "7-0": "RNA-Seq", "7-1": "Files used or generated in RNA-Seq analysis", "8-0": "DNA-Seq", "8-1": "Files used or generated in DNA-Seq analysis" }, "cols": 2, "rows": 9 } [/block] <div align="right"><a href="#top">top</a></div>

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