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Trajectory analysis requires normalized counts as the input data. We recommend our default "CPM, Add 1, Log 2" normalization for most scRNA-Seq data. For alternative normalization methods, see our Normalize counts documentation.

2) Filter to cells that belong in the same trajectory

Trajectory analysis will built build a single branching trajectory for all input cells. Consequently, only cells that share the biological process being studied should be included. For example, a trajectory describing progression through T cell activation should not include monocytes that do not undergo T cell activation.  To learn more about filtering, please see our Filter groups documentation.

3) Filter to genes that characterize the trajectory

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