{"_id":"56d4a10f1c4de4130005d728","category":{"_id":"56d4a0adde40c70b00823ea3","project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","__v":1,"pages":["56d4a10f1c4de4130005d728"],"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-02-29T19:49:01.512Z","from_sync":false,"order":10,"slug":"search-files","title":"SEARCH FILES"},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","__v":12,"user":"554290cd6592e60d00027d17","version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":37,"createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","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"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-02-29T19:50:39.517Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"settings":"","results":{"codes":[]},"auth":"required","params":[],"url":""},"isReference":false,"order":1,"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]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\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>","excerpt":"<a name=\"top\"></a>","slug":"search-files-on-the-cgc","type":"basic","title":"Search files on the CGC"}

Search files on the CGC

<a name="top"></a>

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] <div align="right"><a href="#top">top</a></div> ##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>