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...
▸ Link to code:
https://github.com/kpatel427/YouTubeT...
▸ Other Useful Resources:
What is Demultiplexing? - • A Guide to Next Generation Sequencing...
What is a cell x feature matrix? - • Introduction to single-cell RNA-Seq a... & • How to analyze single-cell RNA-Seq da...
scATAC-Seq packages/tools comparison - https://www.nature.com/articles/s4158...
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/bioinfor...
To get in touch:
Website: https://bioinformagician.org/
Github: https://github.com/kpatel427
Email: [email protected]
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