Search for Data¶
This article explains the Search page and how to use it. All the data you have the permission to access can be reached from here at any time, and you are able to find your samples and collections quickly regardless of the size of the repository. Use our powerful search to validate what was done previously, reanalyze and ask new questions of your data, and compare different datasets.
Basic concepts regarding data levels¶
Each time a process or tool is run on your sample, a data object is generated. For example, if you run an alignment process such as HISAT2 or STAR on your sample, your reads are aligned to a reference genome and a new object is generated consisting of aligned reads and other outputs. These new data objects are linked to your sample.
Now, think of a collection as a ‘container’ to organize your samples. You can group samples by experiment, by batch, or by any other means that makes sense to you. Samples should only exist in a single collection.
There are three tabs on the Search page:
Collections tab, where you search and browse collections
Samples tab, where you search and browse samples
Data Objects tab, where you search and browse data objects
Each tab consists of 3 main elements:
A - Result table
The result table displays all collections, samples or data objects (depending on the selected tab) to which you have access, and each entry is equipped with basic information. Some columns in the table are sortable by clicking on column headers.
B - Search and filtering bar
You can search for your collections, samples or data objects using a query in the search bar above the table. Basic metadata are included in the search index, so you should quickly get to the results. Clicking on the ‘Filtering’ icon button within the search bar will open a dropdown menu with elaborated filtering functionality, from where you can fine-tune your search even further and adjust the columns that you wish to see within the results table by checking the checkboxes next to a specific field. A vast collection of fields is available in the filtering dropdown but the selection varies between the three tabs.
Note that by default all public data such as demo samples and reference data objects (e.g. genome resource files) are visible for you to explore and use when running the analysis. You can hide public data by unchecking the ‘Show public data’ option at the top of the Filtering dropdown menu.
C - A set of quick action icon buttons
Several actions can be performed directly on data, samples and collections by selecting the desired table entries and then using the icon buttons located in the top right corner of the results tables. The icon buttons vary between the three tabs. For more information about data management, visit the Manage Data article.
Collections tab¶
Choose the Collections tab in the Search page. This tab displays a table with all collections to which you have access, and each collection entry is equipped with basic information such as name, date of creation, description, number of samples etc.
Clicking on a collection name will open its Collection Details page. Use this page to learn about the collection details, examine the samples in the collection, examine data objects that are associated with the samples in your collection and run new analysis using a variety of tools and processes.
Quick action icon buttons:
In order to visualize expression results, samples (or whole collections) need to be added to the Sample Basket by first selecting a collection and then clicking the ‘Basket’ icon button.
A new collection can be created from scratch by clicking the ‘Create new collection’ icon button.
Collections can be deleted using the ‘Delete’ icon button. You will be prompted to confirm. Deleting a collection will also delete all its corresponding samples and data objects. Be sure to use this option with caution, as there is no coming back once you delete something.
Samples tab¶
Choose the Samples tab in the Search page. This tab displays a table of all samples to which you have access, and each sample entry is equipped with basic information such as name, date of creation, the collection it belongs to, some quick access links etc.
In addition to the basic information, all analyzed sample entries display additional information in relation to the analysis procedure. The QC column holds the MultiQC report for each sample which you can download and view by clicking on the MultiQC link. The Alignment column and Results column hold sample analysis results which can also be downloaded individually or in bulk using the Download Quick action button.
Clicking on a sample name will open the Sample Details page. Use this page to learn about the analysis history of the sample or to view sample annotations.
Quick action icon buttons:
In order to visualize expression results, samples need to be added to the Sample Basket first by selecting them and then clicking the ‘Basket’ icon button.
Data associated with samples can be downloaded from the samples table by selecting the particular samples and then clicking on the ‘Download’ icon button.
You can create copies of samples and move them to another collection by using the ‘Duplicate‘ and ‘Move’ icon buttons.
Samples can be deleted by using the ‘Delete’ icon button. You will be prompted to confirm. Deleting a sample will also delete all its corresponding data objects. Be sure to use this option with caution, as there is no coming back once you delete something.
Data Objects tab¶
Choose the Data Objects tab in the Search page. This tab displays a table of all data objects to which you have access, and each sample entry is equipped with basic information such as name, type, date of creation, the collection it belongs to etc.
Clicking a data object name will open the
Data Object Details page. Use this page to learn
about the processing history of the data, including its inputs and outputs and
to edit the data object’s name or URL slug.
Quick action icon buttons:
You can create copies of data objects and move them to another collection by using the ‘Duplicate’ and ‘Move’ icon buttons. Note that you can only duplicate or move data objects that have not been created as a result of sample analysis and are therefore not part of any particular sample.
Data objects can be deleted by using the ‘Delete’ icon button. You will be prompted to confirm. Be sure to use this option with caution, as there is no coming back once you delete something.
