Next Generation sequencing data analysis using command line and graphical user interface

Next Generation sequencing data analysis using command line and graphical user interface

October 18, 2022 by Abdul Rehman

Next Generation sequencing data analysis using command line and graphical user interface


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Outcomes of this Training Program:

In these three days, we will bring out to you one of the major bioinformatics concepts of NGS data analysis by understanding the NGS databases and their uses to retrieve data and understanding the Linux Environment installing tools in the Linux environment. Further, we will analyze the data on an online server called GALAXY. Then by using the tools available on galaxy we will analyze the dataset from the SRA database. Gene expression analysis will be done using different tools after that their visualization will be done using a heatmap. Furthermore, we will perform NGS data analysis on the command line as well while handling the files and directories.

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Training Features:
  • Online training with hands-on experience
  • National and international bioinformatics Speakers
  • Questioning/Answering Session
  • Certificate of completion

Topics Covered in the Seminar:

Here is the list of topics that we are going to Cover in the Seminar

Day 1:

Module 1:

  • Introduction of NGS Data
    • NGS Data Concept Explanation
    • NGS Databases
    • Understanding Sequencing
    • Single Cell RNA data analysis Explanation
  • Different Databases for NGS data
    • SRA database for RNA Seq Data
    • GEO database for Microarray data
    • 100x Genomics for Single-Cell RNA
  • Explaining different Concepts of Linux
    • linux introduction
    • Galaxy Server Introduction
    • Explaining different tools for NGS Analysis

Module 2:

  • Understanding the Linux Environment
    • Creating a windows Subsystem
    • Installing tools in the Command line environment
  • Basic Commands for Linux
    • Commands for two handling processes
    • File Handling Commands
    • Process handling Commands
  • Basic usage of databases and Galaxy for data
    • The SRA database use to retrieve datasets
    • Usegalaxy server to analyze the data
    • Command line tools to analyze and import data

Day 2:

Module 1:

  • NGS data analysis using Galaxy server
    • Introduction to SRA files
    • Importing data into Galaxy Server
    • Understanding galaxy webpage
    • Understanding Galaxy objects
    • Importing data directly using the SRA Accession number

Module 2:

  • Gene Expression Analysis
    • Fastqc for Checking the quality Control
    • Trimmomatic for trimming the trim and crop Illumina (FASTQ)
    • Alignment/ Genome Mapping using any tool TopHat Bowtie2 HISAT2
    • Abundance Estimation for FPKM Values retrieval Cufflinks StringTie Feature counts
    • FPKM Value extraction and Calculations
    • Visualizing the values using TBtools

Day 3:


  • Understanding NGS on the Command line
    • Working with directories
    • Working with Files and Formats
    • Agriculture Data Analysis
    • Health Data Analysis


Fee Structure for Webinar:

Fee for the Webinar(for National Students): 2500 PKR only

Easypaisa: 0311-743-7177       Jazzcash: 0309-017-1710

Sada/Naya Pay: 0309-017-1710

Fee for the Webinar(for International Students): 19.99 USD only


    Additional Details

    Webinar Files -

    Event registration closed.

    Date And Time

    2022-11-14 @ 09:00 AM
    2022-11-30 @ 12:00 AM


    Registration End Date




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