DNBC4 scRNA QC
Project description
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 SeriesTM 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
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
Project details
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