When I perform auto-assign bands to normalize my gels, the software doesn't always assign the right bands. I need to do a lot of manual assigning work. Is there a way to optimize this?
Yes. In some cases, especially with MW ladders, where all bands are equidistant, the software can propose an assignment "out of phase". Some reference lanes may also be too distorted to find the correct assignment. In all these cases, first perform a very rough manual assignment, by for instance assigning one band per reference pattern (or just a few reference patterns) to the corresponding reference positions. Click on Show normalized view, and then perform automatic assignment. The program will now ask "Do you want to preserve the existing assignments?". Answer Yes, and the assignment will take into account what you have already done. If the new assignment still doesn't make sense, you can click the Undo button, assign some more bands, and try automatic assignment again.