Genomic Data Analysis NGS data processing on the CLI and GUI

سرفصل های دوره

Hands on tutorial for Transcriptomics/NGS data analysis using GUI and Command line Interfaces

1. Introduction

1. Introduction of Course

2. Bioinformatics Pipelines

2. NGS On Graphical User Interface Using Galaxy

1. What is NGS and why we are using the NGS for data analysis

2. Next-generation sequencing

3. Generations of Sequencing

4. NGS Workflow

5. SRA Database introduction

6. SRA File

7. Galaxy Server Intro to Goals

8. Galaxy Server And Objects

9. Getting Onto Galaxy

10. Tools For NGS Data Analysis

11. Getting SRA Runs from Databases And platform

12. Ncbi Genome to Galaxy

13. Getting Sra Runs To Galaxy

14. Fastqc Tool To Dataset Generated Dataset

15. Trimmomatic Tool On Dataset

16. Alignmentgenome Mapping

17. Abundance Estimation Tool On Dataset

18. From Values To Visuals (Heatmap)

3. CLI in Bioinformatics

1. Introduction and Why CLI in Bioinformatics

2. CLI and GUI Explanation

3. if we already have Graphical user interface system why we should use CLI

4. Short Practical with Programming Language

5. Why Would You Use CLI over GUI

6. Foundation behind CLI Shell explanation

7. Drawbacks of CLI and GUI

8. Linux Introduction and Usage Over years

9. Linux Distros

10. Why Ubuntu Operating System

11. WSL Explanation

12. Linux Vs Unix

13. (Practical) Making A Subsystem For Linux In Windows OS

14. Linux File Handling Commands

15. Accessing And Creating Files In Windows Os

16. Basic Process Management Commands for Linux OS

17. E-utilities on the Linux Command Line

18. Installing NCBI through CLi

19. Entrez Direct Functions

20. Mrna And Protein Seq Retrieval

21. Batch Retrieval of Protein Using Taxon Id

22. Retrieving CDS From Reference Genome

23. Explaining Different Commands

4. NGS data Analysis on Command Line

1. Getting the SRA Reads

2. Checking the Quality of Data

3. Quality Trimming of data

4. Aligners and Aligning Reads to genome

5. SAM and Bam File Indexing and Sorting

6. Feature Extraction

7. Pipeline Code.html

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تولید کننده: Udemy-Training