A consistently documented pipeline is missing

[Leonievb]

A consistent and clear step-by-step pipeline is missing in theREADME.md file. Additionally to the information on how to run the small data set and how to run cellranger for the data from the paper, the following steps should be documented in the proposed order:

• documentation on how to use cellranger + cellranger commands (is already there, should be in the beginning and more detailed)
• Just as comment, not documentation: in this step single cell data should be analysed and low quality cells, especially doublets, removed. Then a list of remaining cells exported in the format:
  "","x"
  1, "CellID1"
  2, "CellID2"
• comment: how to combine clonal with single cell data