I am running a notebook with example for the MAGIC algorithm.
In the data preprocessing step, a filtering operation is required to filter out cells with a small count of transcripts.
My question is twofold:
- Why filtering out cells with a small count of transcripts?
- How to decide the cutoff, i.e. the minimum number of transcripts each cell should have to not be removed from the dataset?
I attach some plots from the original notebook, which display some distributions of the single-cell rnaseq dataset.