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>

GET STARTED

TUTORIALS

ACCESS THE CGC

MANAGE AN ANALYSIS ENVIRONMENT

COLLABORATE SECURELY

DATASETS HUB

PUBLIC PROJECTS

BRING YOUR PRIVATE DATA

SET METADATA ASSOCIATED WITH A PRIVATE FILE

SEARCH FILES

ADD FILES TO A PROJECT

ORGANIZE FILES

ARCHIVE FILES

FIND APPS

RABIX OVERVIEW

DOCKER

DESCRIBE YOUR TOOL (LEGACY)

TOOL WRAPPING TIPS AND TRICKS

EDIT AN APP (LEGACY)

ARCHIVE APPS

RUN AN ANALYSIS

TASK EXECUTION

REVIEW A TASK

VIEW ANALYSIS RESULTS

INTERACTIVE ANALYSIS

DOWNLOAD RESULTS

DEVELOPER TOOLS

CONNECT CLOUD STORAGE

API Hub

API CLIENTS

SB Command Line Interface

API Reference

EDIT AN APP

BULK API ACTIONS

ASYNC BULK ACTIONS

WATCH AND LEARN

DATA CRUNCHER

SBFS (Beta)

SBFS Command Reference