scATAC-seq Data Analysis

Introduction

This repository covers the analysis of scATAC-seq data produced by 10X genomics sequencing. This entry uses the data available from the ArchR publication. Specifically, we use the scATAC-seq data for the cell line mixing experiments. The SRA information is shown below:

SRX9633387: HighLoading
SRX9633388: LowLoading

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Important Resources

10X scATAC Paper

How do you convert a BAM file you found on GEO to the fastq for realignment?

How do you name the Input FASTQ files for 10x pipelines that you downloaded from the internet?

How do you prepare SRA data for CellRanger?

SRA to Seurat walkthrough

Where can I download 10X reference genome data?

Can I use an ARC reference with my scATAC-seq data instead of the scATAC-seq specific reference? Yes!

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Contents

Each section broadly cover different aspects of scATAC-seq data analysis, some more reliably than others...

I. Downloading 10X Data

II. Alignment and Counting with CellRanger

III. Quality Control

IIII. Pseudo-bulk Fragment Analysis