Merging two datasets

I looked at previous discussion about merging two datasets but they don’t apply to my case. So, I am putting the question here: I have two datasets: one is non-tilted and other is titled datasets - so box number and other parameters are the same. The situation is not that complicated. I could have merged the datasets prior to importing to CS but I did not for some reason. It looks like CS can take multiple data in Patch motion correction or CTF estimation job. So, I am wondering which step I should combine both datasets? The earlier step you combine, the better ? Or simply it does not matter?

Thanks for your help best

For tilted/untilted with all else equal, I would merge your (4-8x downsampled) particles prior to 3D classification. It use useful to have separate Patch CTF jobs, in case you want to separate particles again. I usually extract the sets separately (by adding all particles, but just one group of micrographs, as input to Extract).

The idea of merging before initial 3D classification is that your tilted particles may help you recover some rare views from the untilted data.

Dear Dan
Thanks for your advice. I will follow that.