A dataset is a group of files that are linked together in one category.
Datasets could be arranged into hierarchy.
When NGB is opened, you will see a list of datasets in the Datasets panel to the right:
Grouped items can be expanded/collapsed, using an arrow icon next to a group name.
Each item in the datasets hierarchy shows corresponding genome name (e.g. GRCh38, hg19). It is located to the right from the items name.
Each file item in the hierarchy shows its type (e.g. BAM, VCF, WIG, BED, etc.) to left from the file's name.
Data can be opened:
- by clicking a checkbox next to a dataset name - this will open all files, contained in a dataset:
- by clicking a checkbox next to a specific file - this will open only the selected file and the dataset object (reference with annotation):
Data can be closed:
- by unselecting the dataset itself (unsetting the checkbox) - the dataset with its files will be closed:
- by unselecting the file - the file only will be closed. If all files in the dataset are unselected in such way - only dataset object itself will stay opened (reference with annotation):
Note: the NGB has a restriction for maximum allowed count of the inner dataset files that can be opened automatically at once (default value -
10).
If any dataset has more files than this count and the user tries to open such dataset (by clicking a checkbox next to a dataset name) - checkbox will stay unselected, no files will be opened.
When hovering such dataset object - a corresponding warning about large count of files will appear in a tooltip.
User should expand such dataset and select necessary files manually.
Described rules are applied as for simple dataset and for nested datasets (in this case, a number of all files in nested datasets is being counted).If user selects manually any file in this dataset - the dataset checkbox becomes selected too but still disabled:
When you select files from datasets - you can see the following forms in the "Browser" panel:
This view is shown if a dataset has no additional descriptions.
If the one or more VCF files were selected (as on the picture above), the Summary view will show the charts depicting the variations' breakdown as follows:
- by chromosomes (to open a chromosome, click the corresponding bar of the chart)
- by type (click any type to view statistics only by the specific variants type)
- by quality
If no VCF files were selected, the Summary view will only show the list of loaded files:
Dataset may have an html description file:
- If a dataset has a description file - this file is shown in the "Browser" panel by default when opening dataset
- This file is being attached to a dataset during its registration or can be added to the registered dataset separately
- Such file is not displayed in the datasets tree (at the "Datasets" panel)
Additionally to description, each dataset may have any count of notes - text pages attached to the dataset.
This pages are created as plain text notes, Markdown formatting is supported as well.
To create new notes or edit/remove existing ones user shall have the write access to the dataset.
Any user that has access to the dataset, can open and view such notes.
Notes management is organized via the menu in the "Browser" panel header, where user can select what page should be shown in the panel until any position from the reference will be opened.
To create a new note page - click that menu and select the Add note item from the list:
A new form will appear in the "Browser" panel that contains:
- text field to specify a note title
- text field to specify a note content (description)
- buttons to save/cancel note creation
User should specify a title for a note (mandatory), content (optional) and click the SAVE button to create a new note, e.g.:
After, the just-created notes page will appear in the browser:
- note title is shown in the header of the "Browser" panel
- note content is shown in the "Browser" panel,
Markdownformatting is applied - additionally, button to edit the note is shown
Created notes pages are displayed and can be selected from the notes management section in the "Browser" display menu, e.g.:
If user opens a note and then clicks the Edit button for it, a form similar to the note creation one will be opened, where user has the ability:
- to edit a note title
- to edit a note content
- to save/cancel changes
- to remove the note
You may select the view as you wish. For that, use the selector in the "Browser" panel header:
Note: this selector is visible only if the dataset has an own description file.
NGB allows to attach text key-value metadata to datasets and files.
This can be used:
- to create specific tags/labels to datasets or files
- to find datasets and files by their metadata values
- to display tags as dataset/file details (in a tooltip or the summary page)
To manage metadata for a dataset/file - right-click the desired object in the Datasets panel and select the "Edit attributes item" in the context menu:
The pop-up will appear, where user can add/edit/remove attributes for the selected dataset/file.
By default, any dataset/file has no attributes:
Click the Add button to create a new attribute. A new pair of text fields will appear - for a key and a value of the attribute being created:
Then:
- specify a key and a value for a new attribute
- you can click the Add button again to add another attribute
- you can click the cross-button near the Value field to remove the certain attribute
After all changes, click the Save button, e.g.:
Notes:
- there is no ability to save attributes if any of them has empty key or value
- there is no ability to save several attributes for a single dataset/file with the same key (case-insensitive)
Saved attributes can be viewed:
- in a tooltip when hovering over the object:
- in the Summary page of the dataset:
Search in the dataset panel supports the search by attributes (only by values) as well.
If a file/dataset is found by its attribute - near it, the label(s) of the corresponding attribute(s) appear with the selected match, e.g.:
You can download an original file from the files tree in the Datasets panel - use the context menu by the right-click on the desired file:
You can download files related to a dataset and invisible in the files tree (reference and annotation files) in the Datasets panel - use the context menu by the right-click on the dataset itself:
Some simple ways you can view the loaded tracks as follows:
- Click a chromosome's bar in the chart at the Summary view to open the whole chromosome scale in the "Browser" panel:
- Use unified coordinates and search control in the header of the "Browser" panel to open a specific position or a feature (it can be found by the feature name):
- Click a variation in the "Variants" panel to open this variation (load the variation's position) at the VCF track in the "Browser" panel:
- Click a feature in the "Genes" panel to open this feature (load the feature's position) at the GENE track in the "Browser" panel:
Tick or untick a track in the Datasets panel to toggle its visibility in the "Browser" panel.
Each track has the following parts:
- the header that contains the track's type, name and optionally track's menu and actions
- the content of the track
