Scaffold analyses are run in experiment folders, which are indicated with a conical flask icon in the folder tree. To run a Scaffold analysis you need to:
- Create an experiment inside a folder
- Upload files to that specific experiment
- Setup the Scaffold analysis pipeline and run the experiment
To set up your Scaffold analysis, several options need to be configured in the Scaffold analysis popup, including:
- Scaffold* - Scaffolds are utilized by the pipeline for sequence regions, annotations, and validations specifications. Therefore, a scaffold is required to run an analysis.
- Naming scheme - This can be set to Ignore filename if not of interest and this will not affect the output results.
- Reference sequence* - Reference sequence is utilized by the pipeline to annotate your input sequences. Therefore, a reference sequence is required to run an analysis.
- Primer set - This can be set to None if not relevant.
- Numbering scheme - This is used to number antibody amino acid sequences. We currently support Standard, Kabat and IMGT numbering schemes.
Required options to run an analysis are marked with an asterisk (*). Only Admin users can add Scaffolds, Reference sequence, Primer sets, and Naming schemes. This means that before running any analysis with the Scaffold analysis pipeline, an administrator will need to set these up so that all members can access the required information.
Once the Scaffold analysis has been set up, you can run the analysis by clicking Run. Once the analysis starts, a spinner indicating progress will be observable besides Pipeline in the menu tab and the results will be exported into a results folder.
Note that you can select more than one reference sequences by holding down the Ctrl button while selecting the reference sequences.