Hands-on ATAC-Seq Data Analysis for Identification of Chromatin Accessibility Using Linux & R
Course Content
In-depth Introduction to ATAC-Seq Data Analysis
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In-depth Introduction to ATAC-Seq Data Analysis and Its Biology (Chromatin Accessibility, Nucleosomes, Histones)
59:27 -
Selection and Retrieval of Raw ATAC-Seq Reads
20:55 -
What are Raw Reads & What is a FASTQ File
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Introduction to Linux for ATAC-Seq Analysis
22:32
Hands-on ATAC-Seq Data Analysis
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In-depth Theory: Quality Control
19:37 -
Hands-on: Preprocess Raw Reads Using FASTQC, FASTP, Trimmomatic & Cutadapt
27:29 -
In-depth Theory: Mapping (Alignment of Raw Reads)
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Hands-on: Mapping Preprocessed Reads Against a Reference Genome Using BOWTIE2, BWA-MEM
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Hands-on: Deduplication and Post-Alignment Processing
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In-depth Theory: Read Counts & Peak Calling (Chromatin Accessibility Identification)
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In-depth Theory: MACS2 & HOMER
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Hands-on: Peak Calling Using MACS
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Hands-on: Differential Peak Calling Using HOMER
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Theory: Downstream Functional Enrichment Analysis
18:39 -
Hands-on: Gene Ontology Analysis Using topGO & enrichR
14:21 -
Hands-on: Pathways Analysis Using KEGG, PANTHER, Reactome
07:59
Additional Lectures
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Introduction to ArrayExpress
09:55 -
Introduction to Gene Expression Omnibus Database
09:15 -
Gene Expression Omnibus – Platforms
05:33 -
Gene Expression Omnibus – Samples
04:15 -
Gene Expression Omnibus – Series
04:00 -
Gene Expression Omnibus – Datasets
04:44 -
Gene Expression Omnibus – Profiles – How to Search for Gene Expression Profiles
05:55 -
NCBI Genomes & NCBI Assembly
36:14 -
Genome Reference Consortium
07:48 -
Download an Entire Plant Genome & Proteome
26:41 -
How to retrieve an entire genome & Retrieval of SARS-CoV-2 Viral Genome
09:40 -
Genome Assembly Retrieval and Analysis
10:23 -
BED
04:26 -
GTF/GFF
11:06 -
SAM
09:06 -
Introduction to Linux for Bioinformatics
22:32 -
PWD – Print Working Directory
01:26 -
CD – Changing Directories
05:03 -
MKDIR – Making Directories
08:13 -
MV – Moving Files, Directories and Data
05:11 -
Which & Whereis – Find Programs You Installed
03:43 -
RM – Deleting Files and Directories
01:23 -
Find – Finding User Created Files
03:38 -
LS – Listing Files and Directories on Linux
06:45 -
Piping and Redirection of Data
06:34 -
Cat – Visualization and Inspection of Text Data
03:55 -
Head – Reading Specified Number of Lines from Top
03:49 -
Tail- Reading Specified Number of Lines from Bottom
02:23 -
Touch – Modifying File Statistics and Creating Files
07:04 -
Stat – Statistics of File & Directories
02:43 -
Wget – Retrieval of Genome Assemblies
06:48 -
Curl – Retrieval of Bioinformatics Files
02:25 -
Vim – Create and Edit Text Files
05:59 -
Diff – Find Sequence Differences in Files
02:35 -
GZIP – Compress and Archive Files Efficiently
06:05 -
Tar – Create Archives of Genome Data
04:19 -
GUNZIP – Extract Compressed Content
02:14 -
Grep – Finding Uncharacterized Proteins in Human Genome
08:55 -
Cut – Subsetting Required Textual Data from Text Files
05:49 -
Sort – Sorting Data
04:23 -
Uniq – Finding Unique Data Items
10:33 -
WC – Statistics of the Data Within File
02:46 -
CP – Copying Files and Files Contents
03:43 -
Column – Proper Visualization of Delimited Datasets
04:38
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