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 -g

configuration documentationrna_pipeline.cfg

3.Run pipeline

CellCosmo rna pipeline -c rna_pipeline.cfg

4.Detailed docs can be found in manual

• (1) Sample sequencing data preparation
  CellCosmo rna sample
• (2) Demultiplexing FASTQ files with barcode
  CellCosmo rna barcode
• (3) RNA sequence Quality control
  CellCosmo rna cutadapt
• (4) Rna alignment
  CellCosmo rna star
• (5) Quantification of gene
  CellCosmo rna featureCounts
• (6) Cell calling
  CellCosmo rna count
• (7) Cell cluster and web report result output
  CellCosmo rna analysis

Support

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