This tutorial presents an outline of the basic series of steps for analyzing a single cell RNA-Seq experiment in Partek Flow starting with the count matrix file.

If you are starting with the raw data (FASTQ files), please begin with our Processing Single Cell RNA-seq FASTQ Files tutorial, which will take you from raw data to a count matrix file. 

Filtering cells

An important step in analyzing single cell RNA-Seq data is to filter out low quality cells. A few examples of low-quality cells are doublets, cells damaged during cell isolation, or cells with too few reads to be analyzed. 

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