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 or the Data Browser. Once you copy TCGA files to a project, you can follow the steps below to quickly locate them.
On this page:
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.
Click the loupe icon to choose whether the search will only be applied to the current folder or it should also include subfolders.
Once you have set your files' metadata, 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.
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 .
Clicking this icon arranges files by their values for the chosen metadata field.
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.
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.
The tag(s) which are currently applied as a filter will be highlighted in the list of files
For further information about tags on public files and their meaning, please see the table below:
Whole genome sequencing
Whole exome sequencing
Files from the tumor sample
Files from the normal sample
Reference build v37
Files compatible with human reference genome hg19/GRCh37
Reference build v38
Files compatible with human reference genome hg38/GRCh38
Files used or generated in RNA-Seq analysis
Files used or generated in DNA-Seq analysis
Updated 1 day ago