Module: FACS error correction

If subsets of T or B cells are separated by using FACS or magnetic sorting, inaccurate cell separation can occur. To compensate for inaccurate cell sorting errors, IMDA Prep provides a cell subset disambiguation module named FACS error correction. A common example of cell separation is the separation of CD4+ and CD8+ T cells.

Pairs of samples to compare and eliminate their shared clonotypes have to be defined within pairs.txt (see Format Description).

For eliminating potential sorting errors clonotype overlap analysis is performed and clonotypes within 2-fold change (shown in red in Figure 8) are eliminated.

Figure 8: FACS error correction module eliminating shared clonotypes within 2-fold change of two sample as an example for two cell subsets (e.g., CD4+ and CD8+ T cell samples)