How to analyze single-cell ATAC-Seq data in R | Detailed Signac Workflow Tutorial

A detailed walk-through of standard preprocessing steps to analyze a single-cell ATAC sequencing dataset from 10X Genomics in R using the #Signac package. I hope you liked the video. I look forward to your comments under the comments section! ▸ Link to Vignette: https://stuartlab.org/signac/articles/pbmc_vignette#non-linear-dimension-reduction-and-clustering ▸ Link to code: https://github.com/kpatel427/YouTubeTutorials/blob/main/scATACSeq_standard_workflow.R ▸ Other Useful Resources: What is Demultiplexing? - https://youtu.be/OHUDS0qkYiw?t=448&si=QQi5oQVtkiqU93dO What is a cell x feature matrix? - https://youtu.be/xbX49h7BiUU?t=110&si=wHNSf8wtir6UuyIO & https://youtu.be/5HBzgsz8qyk?t=256&si=RCUxPBpbwP0z3MXB scATAC-Seq packages/tools comparison - https://www.nature.com/articles/s41588-021-00790-6 Chapters: 0:00 Intro 00:38 What is ATAC-Seq? 3:52 Difference between bulk and single cell ATAC-Seq 4:46 Applications of scATAC-seq 6:13 scATAC-Seq workflow 10:06 packages/tools to process scATAC-Seq 11:12 Signac vignette and data 11:58 What is a fragment file? 14:13 What does the cell x feature matrix look like? How different is it from scRNA-Seq? 15:32 Creating a ChromatinAssay 16:38 Reading in the metadata 19:00 Creating a SeuratObject 20:20 Add gene annotations to SeuratObject 23:24 Understanding quality control for scATAC-Seq 24:27 What is Nucleosome Signal and Nucleosome banding pattern? 28:01 What is Transcription Start Site (TSS) enrichment score? 28:57 Additional QC metrics 30:33 Compute QC metric 32:52 Visualizing QC 38:42 Filter poor quality cells 39:58 Normalization and linear dimensionality reduction 42:03 Non-linear dimensionality reduction and clustering Show your support and encouragement by buying me a coffee: https://www.buymeacoffee.com/bioinformagic To get in touch: Website: https://bioinformagician.org/ Github: https://github.com/kpatel427 Email: [email protected] #bioinformagician #bioinformatics #signac #atacseq #atac #seurat #singlecell #singler #illumina #bridgeamplification #sequencingbysynthesis #multiplex #alleles #10x #oxfordnanopore #pacbio #affymetrix #barcode #setseed #reproducibility #pseudorandom #singleR #singlecell #annotationdbi #reversestranded #directstranded #strandedness #survival #survminer #survivalanalysis #kaplanmeier #tcga #gdcportal #tcgaportal #nci #cran #bioconductor #funcotator #variantcalling #variants #gatk #vcf #gvcf #haplotype #alleles #geneticvariants #mutations #gff3 #gff #gtf #sam #bam #phred #fasta #fastq #singlecell #10X #ensembl #biomart #annotationdbi #annotables #affymetrix #microarray #affy #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #GEO #rnaseq #ngs