These days, many scRNA-seq is performed using a machine called Chromium, made by 10x Genomics. They also provide a tool called Cell Ranger which can process the FASTQ files and output read count matrices quite easily.

But Cell Ranger does most of the steps automatically. That means it’s hard to tell exactly what’s going on inside.

In this session, we’ll focus on Drop-seq. It’s quite similar to 10x, but the processing steps are more transparent, and there are lots of open-source tools available, as summarised in Dropseq Tools.