Commands:
Generate the pipeline.yml file
scflow main quantnuclei config
Run the pipeline
scflow main quantnuclei make full -v5
Inputs:
Genome reference files Fastq files from 10X experiment pipeline.yml
Steps:
- Builds kallisto index using kb ref
- Performs read quality steps with fastqc
- Performs pseudoalignment using kb count
- Merges the spliced and unspliced matrix using custom python script
Outputs
Kallisto index Fastqc html files Count matrix