Processing Parse Evercode single cell data
Background
Parse Biosciences provides the Evercode platform for single cell
sequencing. This document outlines using the auto-process-ngs
pipeline to perform Fastq generation and QC for Parse Evercode data.
Requirements
No additional external software is required for the Fastq generation or QC.
Fastq generation
The parse_evercode Fastq generation protocol should be used
for Parse Evercode samples when running the
make_fastqs command.
Analysis project setup and QC
Once Fastqs have been successfully generated, the SC_platform
and Library metadata items should be set to the appropriate values
for the Parse Evercode project(s) in the projects.info control file.
The following values are valid options:
Single cell platform |
Library types |
|---|---|
|
|
Running the setup_analysis_dirs command will automatically transfer these values into the project metadata on creation. The run_qc command will then determine the appropriate QC protocol to use based on the metadata values.