distinguishing of broken cells from true low depth cells about cistopic

[wangmeijiao]

ADD: Sequencing depth is an important factor to consider in dimension reduction, clustering and inferring developmental trajectory. It is hard to balance with filtering low quality cells and keeping possible low-depth cells with some biological meanings. I posted my question here in case that others maybe also interested with this question. Please also refer to this thread (stuart-lab/signac#122). cisTopic has a good advantage to treat low-depth cells, which is quite important. I just want to make sure if cisTopic can distinguish low-depth and high-depth cells in one experiment without depth bias.

[cbravo93]

Hi @wangmeijiao !

We have never had issues with depth bias with cisTopic. The number of assignments per cell is proportional to the depth, and are normalised when calculating topic contributions (by dividing by the total number of assignments per cell ('Probability') or using a Z-score).

Hope this answers the question!

C

[wangmeijiao]

Opps! thanks for your response and ... two years later (: . We just filtered out the low quality cells. It seems that cisTopic indeed takes sequence depth into consideration. Thanks again to describe the details inside. @ cbravo93