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Kids First single cell RNA Pipelines

This repo contains tools and workflows for analyzing single cell RNA (scRNA) data from 10X and SmartSeq2

Production Workflows

These workflows are considered acceptable for Single Cell Analysis

10X STAR Solo 2.7.10b Alignment Workflow

Aligns and quantifies 10X single cell data using STAR Solo

Alpha Phase Workflows

These workflows are currently in alpha phase

10X Cell Ranger 6.2.1 Alignment Workflow

Aligns and quantifies 10X single cell data using Cell Ranger

10X Refinement Workflow

Filters and cleans up results from both Cell Ranger and STAR Solo outputs

Smart Seq 2 Workflow

The workflow uses HISAT2 for alignment, RNAseQC to collect sequencing metrics, and RSEM to calculate gene expression. The outputs of the workflow are a matrix of cells gene counts in a loom file, a tarball containing a matrix of the gene counts in Matrix Market format, and a tsv with collected sequencing metrics from all cells analyzed. Basic functionality includes removal of abnormal cells, dimensionality reduction, identification of differentially expressed features, and clustering.

Data are aligned to both the genome and the transcriptome. Genome aligned data are used to collect sequencing metrics and transcriptome aligned data are used to calculate expression.