Single-cell RNA sequencing workflow

This workflow does the following:

1. align reads with STAR to a genome or transcriptome reference
2. gene/transcript quantification with RSEM and/or rpkmforgenes
3. basic qc with RSeQC and MultiQC

Workflow

The figure below illustrates the workflow included in the test directory. Here, use has been made of the additional rule mentioned in Additional advice to generate the transcript annotation gtf.