ATAC-seq

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a high-throughput genomic technique designed to evaluate chromatin accessibility throughout the genome. It leverages a hyperactive Tn5 transposase, which simultaneously cuts and inserts sequencing adapters into regions of open chromatin. This process enables the precise identification of DNA regions accessible to regulatory proteins such as transcription factors.

ATAC-seq has become a widely used tool in epigenetics and functional genomics due to its simplicity, sensitivity, and low input requirements. It is particularly valuable in studies of gene regulation, developmental biology, and disease mechanisms such as cancer, where changes in chromatin structure play a critical role.

Overall, ATAC-seq provides a powerful means of linking chromatin state to gene expression and cellular identity, making it essential for modern studies of genome function and regulation.

By the end of the learning process, students or researchers will be able to explain how ATAC-seq works to profile open chromatin regions. They will be capable of designing basic ATAC-seq experiments, analyzing sequencing data to identify accessible genomic regions, and interpreting the biological significance of those findings. Additionally, they will be able to integrate ATAC-seq data with other genomic datasets to better understand gene regulation and epigenetic changes.

👉 Enroll now and take the first step toward a future in data-driven biology and beyond.

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RNASeq [R]
RNASeq [D]
scRNA-Seq
lncRNA-Seq
miRNA-Seq
PSI-Seq
ChipSeq
ATAC-Seq
scATA-Seq
Spatial Transcriptome
DNASeq
MethylSeq
Whole Genome de novo Assembly
Targeted metagenomics
Whole Genome Metagenomics
Metatranscriptomics
RAD-Seq
SNAP-ChIP

7 Days Training
15 Days Training

Course Information
Course	ATASeq Data Analysis
Duration	online 7 Days Training [ 2 Hours Daily [ Monday To Friday ] ]
Slots	Our working Time is 9:00 AM to 6:00 PM Indian Time Available slots - 9:00 AM to 11:00 AM / 11:00 AM to 1:00 PM / 2:00 PM to 4:00 PM / 4:00 PM to 6:00 PM For training slots after 6 PM or before 9 am as well as weekends training kindly mention during registration accordingly it will be scheduled.
Mode	ðŸ‘‰ For online training candidate have to install ZOOM (with remote control on candidate system which makes 100% interactive) 👉 Run time video recording candidate can make as well as pdf manual will be provided for future reference. 👉 All our training is 100% practical and 100% industrial and 100% interactive which provides same as offline learning. 👉 For doubt clear there will be extra support will be provided based on the requirement. 👉 Certificate will be provided Kindly process with registration and payment from below link and after registration confirmation you will receive email. All our online payment gateway is highly secured. For clarification kindly connect with us on whatsapp or call us on number +91-9673625446.
Sequencing Platform	Illumina
Raw data	Candidate can include maximum 4 datasets of their own during training. Publication standards figures and tables will be generated.
Training Fees
Module-NGS ATASeq Data Analysis	📘 Introduction to Bioinformatics & NGS - What is Bioinformatics? - NGS Technologies Overview - Introduction to ATAC-Seq & Applications - Paired-end Reads, Tn5 Insertion Bias & ATASeq Algorithm 📘 Linux Basics & Environment Setup - Linux Command Line Basics - Installing Tools (FastQC, Bowtie2, MACS2, etc.) - Using Conda and Shell Scripting 📘 Data Retrieval & Formats - Fetching data from NCBI SRA using SRA Toolkit - Understanding FASTQ, SAM, BAM, BED, GTF formats 📘 Read Quality Control - Read Quality Check - Adapter and Quality Trimming 📘 Alignment and Post-processing - Mapping Raw Reads - BAM Processing with Samtools & Picard - Filtering, Deduplication, and Fragment Analysis 📘 Peak Calling - Accurate Peak Calling - Handling Replicates and Tn5 Bias - Paired-end vs Single-end Considerations 📘 Differential Accessibility Analysis - Differential Calculation - Normalization, Replicate Handling, Visualization 📘 Peak Annotation - Annotating Peaks (Downstream, Upstream, Inside Gene, Intergenic) - Genomic Features and Gene Association 📘 Motif Enrichment Analysis - Finding TF Motifs - De novo vs Known Motif Discovery 📘 Footprinting Analysis - Principle of Transcription Factor Protection 📘 Nucleosome Positioning - Estimate Nucleosome Spacing - Fragment Size-based Interpretation 📘 Visualization & Multi-omics Integration - Creating BigWig Files & Viewing in IGV/UCSC - Overlaying ATAC-seq with RNA-seq, ChIP-seq, WGBS data - Integrative Analysis for Functional Interpretation
Preparation	- ATAC-seq : https://en.wikipedia.org/wiki/ATAC-seq - NCBI : https://pubmed.ncbi.nlm.nih.gov/36173566/
Instructor	Industry Experienced
Target Audiance	This course is designed for graduate students, postdoctoral researchers, and professionals working in the fields of conservation biology, evolutionary genomics, and population genetics or any life sciences who are interested in applying genomic tools to real-world conservation challenges.
Contact	Please write us at info@arraygen.com or call or whatsapp us on mobile +91-9673625446 if you need any clarification or for any custom training based on candidate reference paper or candidate own content/tools.

Course Information
Course	ATASeq Data Analysis
Duration	online 15 Days Training [ 2 Hours Daily [ Monday To Friday ] ]
Slots	Our working Time is 9:00 AM to 6:00 PM Indian Time Available slots - 9:00 AM to 11:00 AM / 11:00 AM to 1:00 PM / 2:00 PM to 4:00 PM / 4:00 PM to 6:00 PM For training slots after 6 PM or before 9 am as well as weekends training kindly mention during registration accordingly it will be scheduled.
Mode	ðŸ‘‰ For online training candidate have to install ZOOM (with remote control on candidate system which makes 100% interactive) 👉 Run time video recording candidate can make as well as pdf manual will be provided for future reference. 👉 All our training is 100% practical and 100% industrial and 100% interactive which provides same as offline learning. 👉 For doubt clear there will be extra support will be provided based on the requirement. 👉 Certificate will be provided Kindly process with registration and payment from below link and after registration confirmation you will receive email. All our online payment gateway is highly secured. For clarification kindly connect with us on whatsapp or call us on number +91-9673625446.
Sequencing Platform	Illumina /Ion Torrent/PacBio/Nanopore
Raw data	Candidate can include maximum 4 datasets of their own during training. Publication standards figures and tables will be generated.
Training Fees
Module-I	Advanced Bioinformatics & basic programming
Topics	📘 Introduction to Bioinformatics - Overview of bioinformatics and its applications - Key concepts in computational biology - Role of bioinformatics in genomics, transcriptomics, and proteomics 📘 Understanding NGS and Genomics Bioinformatics - Basics of Next-Generation Sequencing (NGS) - Types of NGS data (RNA-seq, WGS, WES) - Overview of NGS data formats: FASTQ, BAM, VCF - Introduction to pipelines and tools for NGS data analysis 📘 Databases & Data Retrieval (NCBI and UCSC) - Learning how to retrieve biologically correct data - Performing complete batch retrieval (e.g., whole exome) - NCBI: understanding gene-level data retrieval - UCSC: handling large-scale data retrieval - UCSC Genome Browser and Table Browser usage - Batch Coordinate Retrieval and Genomic Data downloads - GFF/GTF gene annotation formats and how to retrieve them - Using BLAT for sequence-based search and alignment 📘 Gene Prediction and Functional Annotation - Gene prediction approaches and tools - Functional annotation using Gene Ontology (GO) - Pathway analysis using KEGG, Reactome - Interpreting gene sets and biological relevance 📘 Standalone/Offline BLAST for Large-Scale Genomic Data - Installing and setting up standalone BLAST - Running local BLAST for batch sequence alignment - Applications in genome-wide homology searches - Custom BLAST databases and performance optimization 📘 PCR Primer Designing and Specificity Check - Designing accurate primers for PCR amplification - Tools: Primer3, NCBI Primer-BLAST - Checking primer specificity using genome-wide BLAST - Avoiding non-target amplification through design best practices 📘 Understanding Python Programming - Introduction to Python for bioinformatics - Scripting basics: variables, loops, functions - Libraries like Biopython, pandas for biological data handling - Automating genomic workflows with Python scripts
AND
Module-II	Next Generation Sequencing (NGS) - ATASeq Data Analysis
Topics	📘 Introduction to Bioinformatics & NGS - What is Bioinformatics? - NGS Technologies Overview - Introduction to ATAC-Seq & Applications - Paired-end Reads, Tn5 Insertion Bias & ATASeq Algorithm 📘 Linux Basics & Environment Setup - Linux Command Line Basics - Installing Tools (FastQC, Bowtie2, MACS2, etc.) - Using Conda and Shell Scripting 📘 Data Retrieval & Formats - Fetching data from NCBI SRA using SRA Toolkit - Understanding FASTQ, SAM, BAM, BED, GTF formats 📘 Read Quality Control - Read Quality Check - Adapter and Quality Trimming 📘 Alignment and Post-processing - Mapping Raw Reads - BAM Processing with Samtools & Picard - Filtering, Deduplication, and Fragment Analysis 📘 Peak Calling - Accurate Peak Calling - Handling Replicates and Tn5 Bias - Paired-end vs Single-end Considerations 📘 Differential Accessibility Analysis - Differential Calculation - Normalization, Replicate Handling, Visualization 📘 Peak Annotation - Annotating Peaks (Downstream, Upstream, Inside Gene, Intergenic) - Genomic Features and Gene Association 📘 Motif Enrichment Analysis - Finding TF Motifs - De novo vs Known Motif Discovery 📘 Footprinting Analysis - Principle of Transcription Factor Protection 📘 Nucleosome Positioning - Estimate Nucleosome Spacing - Fragment Size-based Interpretation 📘 Visualization & Multi-omics Integration - Creating BigWig Files & Viewing in IGV/UCSC - Overlaying ATAC-seq with RNA-seq, ChIP-seq, WGBS data - Integrative Analysis for Functional Interpretation
Preparation	- ATAC-seq : https://en.wikipedia.org/wiki/ATAC-seq - NCBI : https://pubmed.ncbi.nlm.nih.gov/36173566/
Instructor	Industry Experienced
Target Audiance	This course is designed for graduate students, postdoctoral researchers, and professionals working in the fields of conservation biology, evolutionary genomics, and population genetics or any life sciences who are interested in applying genomic tools to real-world conservation challenges.
Contact	Please write us at info@arraygen.com or call or whatsapp us on mobile +91-9673625446 if you need any clarification or for any custom training based on candidate reference paper or candidate own content/tools.