Workflow for the analysis of the synthetic data

The aim of the workflow is to automate the analysis of synthetic data. Inputs and intermediate outputs will be:

Inputs (I#)

• I1. Path to genome sequence file
• I3. Path to gene expression table (csv)
• I14. Output directory
• I16. Pattern specifying the reads file name for an individual cell

Intermediate outputs

• O1. Sampled transcript structures (gtf)
• O11. Files with read-to-genome alignments (bam)
• O12. Path to estimates of gene expression
• O13. Plot with mean vs. standard deviation for individual genes
• O14. Path to table with mean vs. standard deviation for individual genes (csv)
• O15. Plot with initial vs. inferred expression levels for all genes

This will be done as follows:

• Mapping reads to genome (#19)
  • Inputs I1,I14,I16
  • Outputs O12
• Quantifying gene expression (#11)
  • Inputs O1, O11
  • Outputs O12
• MA plot (#12)
  • Inputs O12
  • Outputs O13, O14
• Estimating accuracy of gene expression inference
  • Inputs I3, O14
  • Outputs O16