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 or the Data Browser. Once you copy TCGA files to a project, you can follow the steps below to quickly locate them.

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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.

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Keyword search

Click the loupe icon to choose whether the search will only be applied to the current folder or it should also include subfolders.

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Filter by metadata fields

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.

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Filter by metadata fields

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 .

Clicking this icon arranges files by their values for the chosen metadata field.

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Sort by metadata fields

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.

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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.

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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:

Tag

Description

WGS

Whole genome sequencing

WES

Whole exome sequencing

Index

Index files

Tumor sample

Files from the tumor sample

Normal 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

RNA-Seq

Files used or generated in RNA-Seq analysis

DNA-Seq

Files used or generated in DNA-Seq analysis


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