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Gervaise Henry authored6a95b60c
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README.md 3.15 KiB
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10x Genomics scRNA-Seq (cellranger) mkfastq Pipeline
Introduction
This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
FastQC is run on the resulting fastq and those reports and bcl2fastq reports are collated with the MultiQC tool.
The pipeline uses Nextflow, a bioinformatics workflow tool.
This pipeline is primarily used with a SLURM cluster on the BioHPC Cluster. However, the pipeline should be able to run on any system that Nextflow supports.
Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.