you may opt to enrich by magnetic negative selection first resulting in shorter flow cell sort times which will give higher sort viability.

@Joyce, Thank you for the reply. But my main aim is to make the process "as simple as possible."  I know, by doing as you have mentioned, it will enrich more positive cells that will be better purified by flow in shorter time. But I prefer to use only one of the techniques, cost-effective, but efficient at the same time.

Both procedures are well accepted.  But picking one over the other depends on many things.  The frequency of the population of interest, the ability to define that population for sorting by column vs facs, the downstream application of the sorted cells, the required purity and viability of the sorted cells....  While MACS may be fine for project A, it may be a poor choice for project B and project C may benefit from using both.  A 'simple' answer to your question is not possible!

Both techniques are well accepted and produce almost a similar purity. However, the choice between them depends on the type of stem cell you working with and also the aim of your study. For instance, if you are working with mesenchymal stem cells, it is recommended to culture the discarded sample and bone residual in the sample to salvage more cells.

Thank you for the response (@ Lynda & Saeed). Am working on colorectal cancer stem cells. I like to sort and collect the viable/live stem cells for further downstream processing.