Introduction

The 3' RNA-seq workflow processes single-cell sequencing reads from libraries generated using the ddSEQ™ Single-Cell 3' RNA-Seq Kit (catalog no. 17009671) from Bio-Rad™.

This guide provides information and instructions for using the 3' RNA-seq module of Omnition Analysis Software. Fig. 1 illustrates the single-cell 3' RNA-seq analysis workflow.

Fig. 1: 3' RNA-seq workflow

The workflow processes raw sequencing data into a format suitable for biological interpretation by

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Parsing and correcting single-cell barcodes

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Aligning reads to a reference genome

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Generating count matrices compatible with tertiary analysis tools

To simplify and minimize processing time for high throughput experiments, samples in the workflows are processed in batches for 3' RNA-seq and produce the following outputs:

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Quality control metrics

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Cell clustering information

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Deconvolution metrics

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Cell analysis statistics

Omnition Analysis Software is open-source and available from the following repository in GitHub:

https://github.com/BioRadOpenSource/omnition

For information, see Downloading Omnition Analysis Software.