Tag: ENCODE blacklist hg38 excluderanges
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How to Analyze Single-Cell ATAC-seq Data — A Complete Beginner’s Guide Part 2: Thorough Quality Control with Signac
Separate real nuclei from empty droplets, dead cells, doublets, and artifacts using TSS enrichment, nucleosome signal, FRiP, blacklist ratio, and AMULET. In Part 1 you took raw FASTQ files from a real COVID-19 case/control cohort, ran cellranger-atac count, and ended up with a fragments file, a set of peaks, and a peak-by-barcode matrix. Cell Ranger…
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Recent Posts
- How to Analyze Single-Cell ATAC-seq Data — A Complete Beginner’s Guide Part 2: Thorough Quality Control with Signac
- 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
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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