Reference Based RNASeq

Reference-based RNA sequencing (RNA-Seq) is a widely used method for analyzing transcriptomic data, wherein sequencing reads are aligned to a known reference genome or transcriptome. This approach allows researchers to accurately quantify gene and transcript expression, enabling downstream analyses such as differential gene expression, alternative splicing detection, and gene fusion discovery. It is especially effective in organisms with well-annotated genomes, where it offers high accuracy and efficiency in read mapping and expression profiling.

By leveraging a reference genome, this method reduces computational complexity compared to de novo assembly, and allows integration with known gene models, facilitating biological interpretation. However, it may miss novel transcripts or splice variants not present in the reference annotation.

IMG
By completing the RNASeq pipeline, learners gain practical skills in transcriptome analysis, preparing them for academic research, clinical genomics, or biotech industry roles.

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

## 10% Discount if you register before 15th October, 2025. Hurry up!!

  • 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

Course Information
Course RNASeq - Reference RNASeq / Differential expression / Bulk RNA 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

👉 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

Support

Candidate can also discuss and possible implementation with their own genomic data or any data too during the course.

Module-NGS RNASeq(Ref Based) Data Analysis
    📘 Introduction to Bioinformatics and NGS
    - Definition and scope of Bioinformatics
    - NGS Technologies: Illumina, PacBio, Nanopore
    - Types of NGS Application: RNA-Seq ref based and Understanding of all different NGS applications like chipseq, WGS, metagenome etc
    - Overview of Ref Based NGS data analysis Algorithm and pipeline

    📘 Linux Basics and Tool Installation
    - Basic Linux commands for bioinformatics
    - Installing tools using conda, apt, or source
    - Setup and Install NGS tools

    📘 Data Retrieval and File Types
    - Download data from NCBI SRA or EBI SRA using SRA Toolkit
    - Understanding FASTQ, SAM/BAM, GTF/GFF, FASTA formats

    📘 Read Quality Control
    - Assess Raw read quality
    - Trim adapters and low-quality bases

    📘 Read Alignment
    - Align reads
    - Generate and process SAM/BAM files
    - Post-alignment QC using samtools

    📘 Visualization of Aligned Reads
    - Use UCSC Genome Browser for custom tracks
    - View BAM files in IGV

    📘 Gene Expression Quantification
    - Calculate read coverage and gene counts
    - Compute RPKM/FPKM/TPM

    📘 Differential Expression Analysis (Known and Novel Transcripts Detection)
    - Differential calculation
    - Obtain logFC, p-values, adjusted p-values

    📘 Enrichment Analysis
    - GO and pathway Enrichment analysis
    - GSEA (significantly enriched Analysis)

    📘 Network Analysis (PPI)
    - Use STRINGdb for protein interaction networks
    - Visualize networks in Cytoscape with plugins

    📘 Pathway Mapping using KEGG Mapper
    - Map DEGs to KEGG pathways
    - Visual representation of active pathways (UP and Down regulated Genes)

    📘 Basics of R Programming
    - Data types, control structures, and packages
    - Installing Bioconductor tools

    📘 Coexpression Analysis
    - Introduction to coexpression analysis concepts and tools

    📘 Data Visualization with R
    - Generate Heatmaps, Volcano plots, PCA plots
    - Use ggplot2, DESeq2, ComplexHeatmap

Preparation

- RNAseq Reference : https://en.wikipedia.org/wiki/RNA-Seq
- NCBI : https://pmc.ncbi.nlm.nih.gov/articles/PMC5389949/

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 RNASeq - Reference RNASeq / Differential expression / Bulk RNA 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

👉 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

Support

Candidate can also discuss and possible implementation with their own genomic data or any data too during the course.

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) - RNASeq (Ref Based) Data Analysis
Topics
    📘 Introduction to Bioinformatics and NGS
    - Definition and scope of Bioinformatics
    - NGS Technologies: Illumina, PacBio, Nanopore
    - Types of NGS Application: RNA-Seq ref based and Understanding of all different NGS applications like chipseq, WGS, metagenome etc
    - Overview of Ref Based NGS data analysis Algorithm and pipeline

    📘 Linux Basics and Tool Installation
    - Basic Linux commands for bioinformatics
    - Installing tools using conda, apt, or source
    - Setup and Install NGS tools

    📘 Data Retrieval and File Types
    - Download data from NCBI SRA or EBI SRA using SRA Toolkit
    - Understanding FASTQ, SAM/BAM, GTF/GFF, FASTA formats

    📘 Read Quality Control
    - Assess Raw read quality
    - Trim adapters and low-quality bases

    📘 Read Alignment
    - Align reads
    - Generate and process SAM/BAM files
    - Post-alignment QC using samtools

    📘 Visualization of Aligned Reads
    - Use UCSC Genome Browser for custom tracks
    - View BAM files in IGV

    📘 Gene Expression Quantification
    - Calculate read coverage and gene counts
    - Compute RPKM/FPKM/TPM

    📘 Differential Expression Analysis (Known and Novel Transcripts Detection)
    - Differential calculation
    - Obtain logFC, p-values, adjusted p-values

    📘 Enrichment Analysis
    - GO and pathway Enrichment analysis
    - GSEA (significantly enriched Analysis)

    📘 Network Analysis (PPI)
    - Use STRINGdb for protein interaction networks
    - Visualize networks in Cytoscape with plugins

    📘 Pathway Mapping using KEGG Mapper
    - Map DEGs to KEGG pathways
    - Visual representation of active pathways (UP and Down regulated Genes)

    📘 Basics of R Programming
    - Data types, control structures, and packages
    - Installing Bioconductor tools

    📘 Coexpression Analysis
    - Introduction to coexpression analysis concepts and tools

    📘 Data Visualization with R
    - Generate Heatmaps, Volcano plots, PCA plots
    - Use ggplot2, DESeq2, ComplexHeatmap

Preparation

- RNAseq Reference: https://en.wikipedia.org/wiki/RNA-Seq
- NCBI : https://pmc.ncbi.nlm.nih.gov/articles/PMC5389949/

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.

Refund Policy

Once registration and payment is confirmed there is no refund for the completed registration. Howevevr start dates can be postponed or can be used with other alternate courses.

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.