You can add a SeqMan NGen .assembly package to the session.
Do any of the following:
- Drag & drop one or more assemblies on an open GenVision Pro session
- Press the Add assemblies to project button tool ().
- Choose File > Add Assemblies
For all but the first option on the list above, you will be prompted to select an assembly (or folder of assemblies) from the file browser. After making a selection, press OK. Note that double-clicking is not supported in this situation.
The following table shows warning messages that you might encounter when adding an assembly to a session.
|Please pick an assembly or a directory containing assemblies.||The item selected was not an assembly project or a folder containing an assembly project.|
|Unable to add duplicate data source.||The selected assembly has already been added to the current session.|
|Most of the sequences being added from the assembly “<assembly name>” do not match those in the document. Add data anyway?||Most contigs or chromosomes in the selected assembly do not match those of assemblies already in the session. Click OK to add the assembly anyway, or Cancel to close the dialog without adding the assembly.|
|Feature index not found for assemblies. Index features now?||If this prompt appears, we recommend choosing Yes. Choosing Yes simply causes a “feature index” file to be quickly created and added to the original assembly file package. A detailed explanation of “feature index” appears below this table.|
During assembly, SeqMan NGen 14.0 (and later) automatically includes a features index file as part of the assembly package. GenVision Pro uses the file for rapid access to features. The presence of a features index allows you to navigate to a gene by name and to view features in the Features panel.
An assembly built in an older version of SeqMan NGen will initially lack this feature index. When you add such an assembly to a GenVision Pro session, this message asks whether you wish to have a feature index created automatically. If you click Yes, a file will be created and stored within the original assembly data. If you click No, no file will be created, and the assembly will be added to the session without indexing. This will cause loss of the functionality described in the paragraph above. If you decline to create the feature indices, you may be prompted again when the assembly project is used a different session.
If you add a set of assemblies built using equivalent reference templates, and respond Yes to this prompt, a feature index will be created for just one member of the set. In this case, the genome templates for other members of the set are not loaded into GenVision Pro. Note that if you later add one of the non-indexed assemblies to a different GenVision Pro session, you will again be prompted to index, as the new GenVision Pro session will no longer have access to the indexed assembly. Also, if you add assemblies that have additional chromosomes from those added earlier, one of the “expanded” assemblies will also need to be indexed.
Example: Say you start a GenVision Pro session by adding some human female assemblies from SeqMan NGen v. 13.0. You respond Yes to the indexing prompt, and a feature index is created for one of the assemblies. This index will lack feature indexing for the Y chromosome, since all samples so far are female. If you then add human male assemblies that have the additional chromosome Y, one of the male assemblies will need to be indexed.
Note: In order for GenVision Pro to add the index file, you must have “write” permission for the assembly package. If you do not, someone with Administrator status may need to do this step for you. Alternatively, you can copy to the assembly to a location where you have write permission.
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