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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. 

This tutorial includes only one sample, but the sames steps will be followed when analyzing multiple samples. For notes on a few aspects specific to a multi-sample analysis, please see our Single Cell RNA-Seq Analysis (Multiple Samples) tutorial. 

If you are new to Partek Flow, please see Getting Started with Your Partek Flow Hosted Trial to learn about data transfer, import, and project creation.  

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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