Tag: Cell Ranger ATAC 2.2.0
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How to Analyze Single-Cell ATAC-seq Data — A Complete Beginner’s Guide Part 1: From FASTQ to Peaks
Learn what chromatin accessibility tells you, then take a real 10x Genomics scATAC-seq dataset from raw FASTQ files all the way to a peak-by-cell matrix with Cell Ranger ATAC and MACS3. Prerequisites: Comfort on the Linux command line (navigating folders, running commands) and roughly 100 GB of free disk space. No prior epigenomics or programming…
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Categories
- ATAC-seq (1)
- bulk RNA-seq (27)
- chromatin accessibility (14)
- Database (4)
- Epigenetics (14)
- Genomics (11)
- HPC (6)
- Metagenomics (1)
- Quick Tips (1)
- RNA-seq (20)
- Scientific Programming (6)
- Single Cell Sequencing (21)
- Transcriptomics (28)
Recent Posts
- How to Analyze Single-Cell ATAC-seq Data — A Complete Beginner’s Guide Part 1: From FASTQ to Peaks
- How to Choose the Best Genome Aligner for a Specific NGS Dataset — A Beginner’s Guide to Read Mapping Tools
- How to Set Up a Bulk RNA-seq Pipeline on an HPC Cluster — A Complete Beginner’s Guide to Nextflow and nf-core/rnaseq
- How to Choose Your scRNA-seq QC Tools (Part2-2): SoupX vs DecontX and DoubletFinder vs scDblFinder
Tags
Alternative Splicing Analysis ATAC-seq BAM ChIP-seq chromatin accessibility CNV DESeq2 Differential Expression edgeR FASTQ GATK Mutect2 gene expression heatmap HOMER HPC Isoform limma MACS2 MAF miRNA miRNA-seq MSigDB Normalization peak calling RNA-seq SLURM somatic mutations Transcript VCF whole genome sequencing