Single-cell RNAseq Analysis Central Document

This will be my working document to connect all the datasets and different analysis pipelines together.

Projects

• Dark genes in Galaxea fasicularis
  • Are thermally responsive dark genes (unannotated differentially express genes) cell type specific?
  • Can we use dark genes as cell markers in corals and other non-model organisms?
• Functional characterization of immune cells in Mnemiopsis leidyi
  • Can we functionally characterize putative innate immune cells (phagocytes) in the marine invertebrate Mnemiopsis leidyi?

Bioinformatic pipelines and troubleshooting

• Example of a general CellRanger workflow
  • Workflow is linked here
• Comparing mitochondrial genome integration methods
  • Workflow and results are liked here
• “Barnyard” approach to map Symbiodinaceae and coral reads in CellRanger
  • Workflow is liked here