DNBC4-test 1.0.5

DNBC4 scRNA QC

DNBelab_C_Series_HT_scRNA-analysis-software

An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets

Introduction

• Propose
  • An open source and flexible pipeline to analyze DNBelab C Series^TM single-cell RNA datasets.
• Language
  • Workflow Description Language (WDL), Python3 and R scripts.
• Hardware/Software requirements
  • x86-64 compatible processors.
  • require at least 50GB of RAM and 4 CPU.
  • centos 7.x 64-bit operating system (Linux kernel 3.10.0, compatible with higher software and hardware configuration).
• Workflow

Directory contents

• config Read structure configure files
• database database include fasta,gtf,star index
• scripts Miscellaneous scripts
• software Software required in the process
• workflows WDL pipeline

Installation

installation manual here

Software

• PISA
• STAR

Database

Creat database manual here

config JSON file

An config JSON file includes all input parameters and genome reference index directory for running pipelines. Always use absolute paths in config JSON.
config JSON file specification

Start

• Setup configure file.
  Copy config.json from the example to the analysis directory and replace it with the real path and fastq path.
  Copy run.sh from the example to the analysis directory and replace it with the real path.
• Run the pipeline

### run the pipeline
sh run.sh
### Background run the pipeline
nohup sh run.sh > run.log 2>&1 &
### run in Cluster(sge)
echo "sh run.sh" | qsub -cwd -l vf=50G,num_proc=4 -q xxx -N scRNA_run
### run in Cluster(pbs)
echo "sh run.sh" | qsub -d $(pwd) -l nodes=1:ppn=6 -q xxx -N scRNA_run

FAQ

Frequently Asked Questions here