Single-cell RNA sequencing (scRNA-seq): filtering cells by transcript counts, how to choose cutoffs?

Question

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.

Answer 1

By reading this tutorial:

Wells with few reads/molecules are likely to have been broken or failed to capture a cell, and should thus be removed.

This answers the first part of the question.

For the second part, i.e. how to decide cutoff, it still seems a bit arbitrary to me, but some authors trim the cells on the left tail of the highest mode, in order to remove other modes (likely due to noise) on the left tail, considering the distribution of cells dependent on the sum of reads (molecules per cell, first plot).