Single Cell Pipeline

We provide here our most up to date pipelines for processing and analyzing single cell and single nucleus RNA-Seq data. Our pipelines utilize Cumulus and the Terra cloud platform environment. You can read more about our updated pipelines in our recent COVID-19 paper. The pipeline performs our preprocessing steps and initial sc/snRNA-Seq analysis steps.

Our pipeline includes a python script to facilitate rapid execution of the following:

• Cellranger mkfastq (for demultiplexing the sequencing data to fastq files)
• Cellranger count (for generating the raw counts matrix)
• Cellbender remove-background (for removing ambient RNA and empty droplets)
• Cumulus pegasus (for data preprocessing and early analyses)

The python script is intended to be run from a compute cluster and generates directories on both your local cluster and in the Google Bucket linked to your Terra Workspace. The script utilizes a master tracking sheet and stores input files for the steps listed above on both your cluster and in your Google Bucket. The script will generate commands you can use to run Cellranger mfkastq, Cellranger count, Cellbender remove-background and cumulus right from your command line, or files you can use to run these steps with the user interface on Terra.

Python script to run entire pipeline and required input sample tracking sheet.

In the main folder, we also provide the sample sheets and json files created by the python script . json files are named input*json and sample sheets are named samplesheet*csv.