Final Project - single cell RNAseq

For the final project, you will be processing single cell RNAseq data from a published experiment. Your workflow will need to convert the provided BAM files back to FASTQs and re-align the reads to an appropriate reference genome. We have provided you with a docker image containing the latest version of cellranger, but you may also explore other valid alignment strategies (STARsolo, etc.).

Once you have a successfully working pipeline, you will need to perform a basic analysis of the data in either Seurat or Scanpy. These directions will only give you a basic scaffold of what you need to do and the rest you will need to implement on your own.