The Features view provides a table that allows you to view and manage all of the features within a selected contig. Checking and unchecking features in the view partially determines which features can be seen in the Alignment and Strategy views. (Feature display is also dependent on which tracks are visible).
To access the Features view, choose one or more contigs from the Explorer panel. Then either choose View > Features > (Contig Name) or Features > (Contig Name; or right-click on the selected contig(s) and choose Show Feature Table.
If you select multiple contigs, a separate Features view will open for each of them. If you select “Unlocated Contigs,” individual tables will open for each member of the group. You may wish to avoid selecting “Unlocated Contigs” if you are working with a large number of such contigs, as with many transcriptome or multi-chromosome genome assemblies.
The following table describes each of the columns in this view:
|Show||Boxes with/without checkmarks are visible/hidden in the other views. Add or remove check marks by clicking the boxes.|
|Location||The sequence range where the feature is located.|
|Sequence||The name of the contig containing the feature.|
|Target Length||The length of the feature in bases.|
|Coverage Depth||The average depth of sequence coverage along the length of the feature.|
The table below shows tasks that can be done in the Features view:
|Choose which features appear in the Features view|| Use the drop-down menu on the left of the Features view header to show increasingly specific tables of features: All Features, Genes (only) and the subset of feature types chosen on the Input Reference Sequences page of the SeqMan NGen wizard (e.g. CDSs and ncRNAs only).
|Select all features of a specified type||Select a type of feature from the Features view (e.g., a CDS feature) and then use the menu commands Features > Select > Select All Selected (or Select All of Type or Select Only of Type ).|
|Choose which features appear in the Strategy view|| To choose which features should be shown or hidden in the Strategy view when Feature tracks are displayed, add or remove checkmarks from the features in the Features view. As a shortcut, you can use the following commands to add or remove checkmarks in groups.
|Add, rearrange, rename, or remove table columns||Press the Change options in this view tool ( ) in the top right of the view. For instructions and a description of each column type, see Customize tables in the views.|
|Export data from the table||Press the Export data tool ( ) in the top right of the view. This opens a save dialog in which you can save the tabular data in comma-separated (.csv) or tab-separated (.tab) format.|
|View features for constituent sequences||Display the Features track in the Alignment or Strategy views. If you are unable to see an expected feature, it may have been on part of the sequence that was trimmed as vector.|
|View features on the consensus sequence||Display the Features track in the Strategy view.|
|Simultaneously select a feature in multiple views.||When you select a feature in the Features view, the range of the feature will also be selected in the Alignment view, for features on constituent sequences; or the Strategy view, for features on the consensus sequence.|
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