Single-cell RNA sequencing workflow

This workflow does the following:

  1. aligns 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
  4. filters out failed cells based on the qc stats and generates a report

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.

_images/scrnaseq.png