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:
stuartlab.org/signac/articles...
▸ Link to code:
github.com/kpatel427/TH-camT...
▸ Other Useful Resources:
What is Demultiplexing? - • A Guide to Next Genera...
What is a cell x feature matrix? - • Introduction to single... & • How to analyze single-...
scATAC-Seq packages/tools comparison - 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:
www.buymeacoffee.com/bioinfor...
To get in touch:
Website: bioinformagician.org/
Github: github.com/kpatel427
Email: [e-mail]
#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

[@PsycheSnacks657]

The best TH-cam channel to learn bioinformatics

[@jawad7776]

I can only wish to reach at the level of expertise you have...

[@johncruise6989]

Relevant question, If you do not have the `.h5` file, and have
data that is formatted as three files, a counts file (`.mtx`), a cell barcodes
file, and a peaks file. how should i laod the data and also what about fragments file ?

[@parnakanodia2262]

Hi thank you for your effort and attention to detail in creating these videos, could i please request you to see if you can post a lecture on "how to remove duplicates from fastq files using oxford academic's Bioinformatics' Minirmd 2021 tool(or anything else you feel would work better)? And kindly mention how/where in the RNAseq pipeline it would fit in heirarchy

[@aidaht1]

I really needed this😍thanks a lot❤️

[@arlenjamesmosqueraruiz957]

Nice tutorial. I have seen all of your videos and I have learned a lot! Thankss

[@mohammadyaghmoury1996]

another awesome tutorial. Keep up the good work.

[@samanwoymukherjee4945]

This is awesome Khusbu! As always 🎉 can you please cover Perturbseq and CiteSeq too

[@yqh7297]

Could you make some videos about drug target mendelian randomization?

[@SAMUTHIRAPANDISUBBURAJ]

It's really understandable and helpful for beginners in bioinformatics research like me. I request make class about data analysis for Copy Number Variation (CNV) and Structural Variation (SV)?.

[@soumitadas6468]

Can you pls tell how to find promoter region in prokaryotic system?

[@manushreesharma5793]

Hello Ma'am. Love your videos. I was hoping you could help me with a certain thing. So I had 5000+ protein sequences of a bacteria. I ran them on InterPro and obtained the tsv output. I obtained data such as GO annotations and pathway annotations. Now I need to find the function of these proteins. I am unable to figure out how to exactly proceed from here on. Could you please help me?

[@Wuhan.Huazhong]

can you make a sperate video tutorial on bulk ATAC-seq data analysis through linux operating system from very basics like to create environment and installation of software from where we can pick them up, and different file format. peak calling, differential accessible regions and if possible to integrate them with RNA-seq DEGs

[@oludelehalleluyah6723]

You're good. Please I want to learn bioinformatics very well. Can you give me list of textbooks I can read?

[@Po0pypoopy]

Chatgpt is pretty good at explaining things
Just Google bioinformatics books and read some of them then ask ChatGPT to explain it further with examples