Some Quick Details About MagpieMagpie is a computational pipeline that both biologists and informatics specialists can use to produce qualitative and quantitative evaluations of gene editing experiments. We designed the pipeline to integrate with your company’s existing enterprise content management platform or data storage system so that your data and analytics reside in the same environment and are always secure, accessible and centralized. Magpie can process numerous files in a parallel and threaded fashion completing a large analysis in under an hour that would typically require multiple business days. Yes, it’s that fast. Importantly, we can version lock your company’s Magpie preserving configuration and parameter settings to ensure that the pipeline you run today to generate data for regulatory filings can be re-run in its exact form at any future date. In addition, Magpie comes with tunable cleavage offsets so you can configure the pipeline to accommodate the specific requirements of your proprietary nucleases. Finally, you can initiate a batch run, go about your other work, and be notified when the analysis is complete and reports have been generated. You don’t even need to be logged into your Catalytic Platform for your analysis to complete once it’s initiated.
Running Magpie Is This Easy!
Get started by navigating to your Analytics tab on your dashboard, locate the Magpie tile and click to open.
To simultaneously run multiple ‘Paired-End’ or ‘Single End’ analyses, upload the files to the ‘Files List’ by clicking
A file picker will open that allows you to choose the appropriate files from either your ‘folders’ (in this case these are your Box folders) or from local storage on your computer.
Once files are uploaded, you can simply drag and drop the files to the desired Forward or Reverse runs window if performing a paired-end run or choose Single if performing a single end run. Alternatively, you can select the files you want to move by checking the box to the left of the file and selecting the filter dropdown to move selected files to Forward, Reverse or Single runs window.
We’ve also made it easier for you to find and select files that share a common identifier. For example, if your paired reads are named with a common identifier, such as -F or -1, you can filter these files by a specific identifier and only those files with the presence of this identifier will appear in your list. You can then choose “Select all” and move selected files to Forward, Reverse or Single runs window or simply drag and drop files to Forward, Reverse or Single runs window.
After adding files, remove the filter and the files that were not moved reappear in the Files List window.
Next, enter the amplicon sequence by typing, pasting or clicking the button to import a file from your folders or computer.
Change the optional parameters or leave them at default settings. Click “SUBMIT” to initiate the analysis.
The analysis will begin processing.
Click “View Results” to see your graphical output displayed in the modal window. You can scroll through the results using the scroll bar on the right side of the window.
Now that you have your results, you can save them to a designated folder by checking the box on the left side destination folder. Once you’ve selected the file(s) you wish to save to your folders and the destination, click above “Status”. Your results are now saved. Alternatively, you can click the sign to enable a new folder to be created. If creating a new folder, simply name it and select “Choose”.
You can now find, access and share your saved results anytime by navigating to the Folders Tab on your Catalytic Platform or by searching the file name from your Catalytic Platform search box.
If you are ready to run a new analysis, simply click ‘NEW RUN’ to the right of ‘SEND TO FOLDERS’.
Once selected, a message box will appear to double-check if you really want to initiate a new run or return to your current results.
You can ‘CANCEL” and return to your results page or click “CONTINUE” to perform a new run.
If you would like to learn more details about Catalytic’s Magpie release or see it live in a demo please contact us and our team will be happy to help.