Genomic Data Analysis Reads-> Variants Bioinfo Unix Pipeline

سرفصل های دوره

Hands on Bioinformatics Pipeline Implementation for Calling Variant’s on Linux OS and WSL on windows

1. Introduction

1. Introduction of Course

2. What is Bioinformatics Pipeline

2. Understanding Command Line for 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

3. Variant Calling Pipeline

1. Variants and Types

2. Understanding the Metadata and Softwares

3. Getting Data From SRA Using SRA Toolkit

4. Quality Control and Trimming

5. Sam and Bcf Tools and Fixing NS and Calling Variants

6. Alignment to Reference Genome

7. Separation of SNPs and Indels Variants

8. Visualizing Variants Using IGV and UCSC Browser

9. Pipeline Code.html

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تولید کننده: Udemy-Training