{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","settings":"","params":[],"results":{"codes":[]}},"next":{"description":"","pages":[]},"title":"Search files on the CGC","type":"basic","slug":"search-files-on-the-cgc","excerpt":"<a name=\"top\"></a>","body":"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. \n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"On this page:\",\n  \"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)\"\n}\n[/block]\n##Keyword search\n\nYou 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.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/JEN1WYRwTDSRsG4dGOsW_filter%20files.jpg\",\n        \"filter files.jpg\",\n        \"1883\",\n        \"715\",\n        \"#0f58a5\",\n        \"\"\n      ],\n      \"caption\": \"Keyword search\",\n      \"border\": true\n    }\n  ]\n}\n[/block]\nClick the loupe icon to choose whether the search will only be applied to the current folder or it should also include subfolders.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/9a2e202-search-files-on-platform-cgc.jpg\",\n        \"search-files-on-platform-cgc.jpg\",\n        687,\n        343,\n        \"#e3eaee\"\n      ]\n    }\n  ]\n}\n[/block]\n##Filter by metadata fields\n\nOnce 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.\n\nYou can add additional drop-down menus to filter by other metadata fields by clicking the **+** icon. \n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/Bb6wI8RhQE2a1AJMlUIC_filter%20cgc.jpg\",\n        \"filter cgc.jpg\",\n        \"1617\",\n        \"715\",\n        \"#1258a2\",\n        \"\"\n      ],\n      \"caption\": \"Filter by metadata fields\"\n    }\n  ]\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Sort by metadata fields\n\nYou 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. \n\nYou 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\"\nheight=\"20px\" width=\"auto\" align=\"inline\" style=\"margin:1px\"/>.\n\nClicking this icon arranges files by their values for the chosen metadata field.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/1dc5dcd-Screen_Shot_2016-12-15_at_11.29.20_AM.png\",\n        \"Screen Shot 2016-12-15 at 11.29.20 AM.png\",\n        708,\n        537,\n        \"#f6f6f5\"\n      ],\n      \"caption\": \"Sort by metadata fields\",\n      \"border\": true\n    }\n  ]\n}\n[/block]\n##Filter by tags\n\nPublic 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.\n\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/34e3a08-cgc-filter-by-tags.png\",\n        \"cgc-filter-by-tags.png\",\n        746,\n        607,\n        \"#e8ebeb\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\nYou 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.\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"The tag(s) which are currently applied as a filter will be highlighted in the list of files\"\n}\n[/block]\nFor further information about tags on public files and their meaning, please see the table below:\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Tag\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"WGS\",\n    \"0-1\": \"Whole genome sequencing\",\n    \"1-0\": \"WES\",\n    \"1-1\": \"Whole exome sequencing\",\n    \"2-0\": \"Index\",\n    \"2-1\": \"Index files\",\n    \"3-0\": \"Tumor sample\",\n    \"3-1\": \"Files from the tumor sample\",\n    \"4-0\": \"Normal sample\",\n    \"4-1\": \"Files from the normal sample\",\n    \"5-0\": \"Reference build v37\",\n    \"5-1\": \"Files compatible with human reference genome hg19/GRCh37\",\n    \"6-0\": \"Reference build v38\",\n    \"6-1\": \"Files compatible with human reference genome hg38/GRCh38\",\n    \"7-0\": \"RNA-Seq\",\n    \"7-1\": \"Files used or generated in RNA-Seq analysis\",\n    \"8-0\": \"DNA-Seq\",\n    \"8-1\": \"Files used or generated in DNA-Seq analysis\"\n  },\n  \"cols\": 2,\n  \"rows\": 9\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>","updates":[],"order":1,"isReference":false,"hidden":false,"sync_unique":"","link_url":"","link_external":false,"_id":"56d4a10f1c4de4130005d728","category":{"sync":{"isSync":false,"url":""},"pages":["56d4a10f1c4de4130005d728"],"title":"SEARCH FILES","slug":"search-files","order":10,"from_sync":false,"reference":false,"_id":"56d4a0adde40c70b00823ea3","project":"55faf11ba62ba1170021a9a7","createdAt":"2016-02-29T19:49:01.512Z","version":"55faf11ba62ba1170021a9aa","__v":1},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","__v":12,"user":"554290cd6592e60d00027d17","version":{"version":"1.0","version_clean":"1.0.0","codename":"","is_stable":true,"is_beta":true,"is_hidden":false,"is_deprecated":false,"categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f","5c222bed4bc358002f21459a","5c22412594a2a5005cc9e919","5c41ae1c33592700190a291e","5c8a525e2ba7b2003f9b153c","5cbf14d58c79c700ef2b502e","5db6f03a6e187c006f667fa4","5f894c7d3b0894006477ca01"],"_id":"55faf11ba62ba1170021a9aa","releaseDate":"2015-09-17T16:58:03.490Z","createdAt":"2015-09-17T16:58:03.490Z","project":"55faf11ba62ba1170021a9a7","__v":47},"createdAt":"2016-02-29T19:50:39.517Z","githubsync":""}