FlowJo requires two files to work properly: .WSP and .FCS. The .WSP is a “workspace” file where users make adjustments (compensations, gating, etc.), but they must point to specific paths where the actual data (.FCS) files live in order for the FACS plots to show up.
Solution: FlowJo gives you the option to save the .WSP and .FCS files into one single file called an .ACS file. If users export this file type and upload to Benchling, then Benchling Sync works as normal.
There are also two other options to work with FlowJo.
Option 1: Create WSP with appropriate FCS mappings. Upload only the WSP to Benchling and use the Benchling Sync desktop app as normal. Note: The mapping will break if another user tries to checkout the file on a different computer.
Option 2: Upload the WSP to Benchling as well as all of the FCS files. Checkout the WSP file. Download the FCS files (can put in a .zip for ease) and re-establish the mapping within FlowJo.