Why register entities in bulk, rather than individually?
You can register DNA / AA sequences in two ways: single registration or in bulk.
- The single registration process works well for registering 3 or less entities. You'll import your entity, fill out metadata, register, and then create new batches.
- The bulk process works well if you need to register many entities. You'll import metadata and batch information, import DNA or AA maps, and then register. This is the focus of this article.
Create a spreadsheet with entity data
You may often have multiple files that need to be registered. In this case, you'll need to use an Excel template to prepare your data.
We will walk through an example of a bulk sequence re-import. To do so, you must prepare an Excel template with the data.
Generate the spreadsheet
- The spreadsheet needs a Name column. The values in the column need to exactly match the name of your DNA / AA sequence files from Snapgene, Geneious, or other softwares.
- The spreadsheet should have a column for Bases or AA. You'll keep this blank for now since we'll reimport our sequence maps in a later step.
Importing entities from a spreadsheet
- Open your project folder. Toggle to the Inventory Section. Click “+” and select Import Entities.
- Select your DNA / AA schema from the schema dropdown. Click Next.
- If you want to create batches at this time, we suggest you check off the box Create Batches with Entities. Benchling will create batches at the same time as entities.
- If you are using Sample Tracking [Industry only] and would like to simultaneously create a container and deposit into a Sample Management Location (i.e. Box), then select Create Containers with Input Batches and designate the container schema.
- In the following window, select Raw Text option from the dropdown. Go back to your Excel template and copy out the data. Make sure to include the headers. Paste this into the Import modal. Click Next.
- Benchling will map the column headers to schema fields in the registry. If you used the above template, Benchling will autodetect the correct fields. Once confirmed, click Next. Note: if you selected the create batches, Benchling will map Batch fields from the Excel sheet.
- In the next modal, Benchling will check for errors. If there are errors, you can select the files and click Remove Files or may be required to make modifications in your Excel sheet. Note: the most common error will likely be that you're missing the Bases column from your Excel sheet. Again, this should be blank but Benchling expects a column header for Bases or AA.
- Once complete, hit Import. These entities and batches should now be in the project you imported them to. Find the project and expand the view by selecting the Arrow on the top right of the side panel. If you click into an entity, you'll notice that you won't see any sequences for that entity.
Reimport your DNA / AA sequences
Now it's time to import your sequence map to the Benchling registry. Click the "+" sign and then select Reimport DNA or AA Sequences.
In the new modal, you can now drag and drop in your sequence files. You need to make sure that the file name is the same as the entity name in Benchling. Once you drop all the files, select import. Each sequence file should also contain only ONE sequence per file as Benchling will generate an error if multiple sequences are found on one sequence file.
Register your sequences
Register your sequences by expanding the side panel, selecting your entities of choice, and then hitting Register.