Inquiry Regarding Incorrect Assignment of Root Cells to Termini During URD Trajectory Tree Construction (Despite Normal Pseudotime Results) #91
Description
Dear Colleague,
I encountered a critical issue while performing cell differentiation trajectory analysis using URD. Specifically, the pseudotime calculation results are consistent with expectations: the pseudotime values of the designated root cells (e.g., the NCC subpopulation) are significantly lower than those of terminal cells, clearly reflecting the biological logic of "differentiation start (root) → end (terminus)".
However, during the subsequent construction of the differentiation tree via the buildTree function, a large number of the originally designated root cells were incorrectly assigned to the "terminal cell" category. This ultimately led to an almost complete absence of identifiable root cells in the resulting trajectory tree, severely compromising the accuracy of the inferred differentiation pathways.
I would greatly appreciate your insights on the following: Given that the pseudotime results themselves are normal, what could be the potential causes for the erroneous assignment of root cells to termini during tree construction?
