Mixed base space and color space mappings

For mixed data sets consisting of base space data and color space data, we recommend the following approach:

  1. Run a mapping using the clc_mapper tool using the base space data.
  2. Run a mapping using the clc_mapper_legacy tool using the color space data and the exact same reference sequence set used for the base space mapping.
  3. Join these mappings using the clc_join_mappings tool.