Introduction | Case Study: Preprocessing CEL-seq2 data | Getting started | Organising the files required | Data Preprocessing | Fastq reformatting | Aligning reads to a reference genome | Assigning reads to annotated exons | De-multiplexing data and counting genes | Preprocessing data generated by other protocols | Quality Control | Downstream analysis

Introduction | Workflow | Getting started | Fastq reformatting | Aligning reads to a reference genome | Demultiplexing the BAM file | Remove duplicates | Gemerating a fragment file | Peak calling | Assigning reads to features and feature counting | Generating the Single-cell Experiment (SCE) object | A convenience function for running the whole pipeline | Downstream analysis | Session Information