Introduction

CellCosmo is an open source and bioinfomatics analysis pipeline to high-throughput analysis Perseus Series single-cell RNA datasets.

• Propose
  • A collection of bioinfomatics analysis pipelines to process single cell sequencing data generated with Perseus Series single-cell RNA products.
• Language
  • Python3(>=3.9.*)
  • R scripts
• Hardware/Software environment
  • x86-64 compatible processors.
  • require at least 30GB of RAM and 4 CPU.
  • centos 7.x 64-bit operating system (Linux kernel 3.10.0, compatible with higher software and hardware configuration).

Installation

Installation tutorial manual here

Start Running CellCosmo

1. Build References genomeDir for Homo sapiens or Mus musculus

Build References genomeDir tutorial manual here

2.Generate configuration file(rna_pipeline.cfg)

Run the following command to get the cfg file:

CellCosmo rna pipeline -t starsolo -g 

• Detailed configuration documentationrna_starsolo_pipeline.cfg
• If already established References genomeDir and Kit version1 default, You can apply the simplified version of configuration documentationrna_pipeline_sv.cfg

3.Run pipeline

CellCosmo rna pipeline -t starsolo -c rna_pipeline.cfg

4.Detailed docs can be found in manual

• (1) Sample sequencing data preparation
  CellCosmo rna sample
• (2) Rna alignment CellCosmo rna starsolo
• (3) Cell cluster and web report result output
  CellCosmo rna analysis

Support

The officially supported release binaries are available at: (http://www.10kgenomics.com/)