The goal of this repository is to implement pipeline to analyze a RNA Single Cell Seq data from the Illumina Bio-Rad ddSEQ single Cell Isolator. An open tutorial written by Vladimir Kiselev on genomic format processing regarding RNA Single Seq data can be found here, the following image is taken from that source.
The RNA Single Cell Data used to implement this pipeline consists of pair ended sequences from murine mESC cells publicly available here. See the full documentation of this workflow here.