Bioinformatics Ka Chilla
Quiz No. 1: Linux and Conda Quiz
Bioinformatics Ka Chilla
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00: Resources
Bioinformatics ka Chilla - LMS Access terms and conditions
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Discord Server
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Linux/Unix Cheatsheet
Reading
GitHub repo for this course
Reading
01: Course Introduction and Registration
Course Introduction: Bioinformatics Ka Chilla | A Complete Course on Bioinformatics
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Bioinformatics Ka Chilla | Complete Registration Process for Bioinformatics Course
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02: Know your Instructor
Know Your Instructor for Bioinformatics Ka Chilla | Meet the Expert Behind the Bioinformatics Course
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03: What is Bioinformatics?
Introduction to Bioinformatics for Beginners | Learn Biological Data Science in Urdu | Codanics
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04: Coding for Bioinformatics
GUI vs CLI for Bioinformatics & Data Science: Which One Should You Choose?
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Tip for Programmers or Coders for Bioinformatics: Automate Tasks and Focus on Scripting
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3 Essential Skills to Become an Expert Bioinformatician | Must-Know Skills for Bioinformatics
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05: Linux-Everything you need to know
Intro to Linux and Linux Distributions for Bioinformatics and Data Science
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Linux Mint Installation as virtual machine in virtual box in windows
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Linux Mint Installation Guide for Bioinformaticians A - Z in Urdu | Codanics
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Keep Your Linux Mint Up to Date with These Easy Commands & Tips | sudo apt update & upgrade
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Screen resolution and font size settings in linux mint
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Startup applications in linux mint can speedup your linux PC
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Install latest codecs and fonts plus extras in linux mint
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Firewall configuration on linux mint for everyone
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Pannel taskbar and folder settings in linux mint
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Keyboard shortcuts to launch panel apps in linux mint
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Night light settings for blue light filter in linux mint using redshift
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TLP package to optimize battery life of linux laptop
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Hot-corners in linux mint for mouse shortcuts
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Mouse / touch pad gestures in linux mint
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Workspaces in linux mint and touchpad gestures
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Desktop zooming options in linux mint for better understanding
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Keyboard Shortcuts for linux mint
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Software manager settings for better results in linux mint
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Install google chrome or any other software for linux mint
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Applets and Desklets in Linux Mint to make your desktop amazingly charming
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Linux Mint Extensions for Desktop Beautification and professional look
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Desktop settings and icons on linux mint
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Basic Linux commands in Linux Mint terminal (Part-1)
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Paths and Working directories in Linux Mint
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Basic Linux Commands in Linux Mint (Part-2)
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File Permission chmod Commands in Linux Mint | Manage File Access Efficiently
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Combining Commands & Using -y Option in Linux Mint | Beginner-Friendly Linux Tips
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Create Your First Shell Script and Execute It in Linux Mint | Beginner Shell Scripting Guide
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Create a Shell Script Using Terminal + wget Command in Linux Mint | Automate File Downloads
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Combine Content of Two Files into One & Write Terminal Output to File in Linux Mint | Easy Guide
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View Large Files Using less, more, head, and tail Commands in Linux Mint Terminal | Easy Tutorial
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grep Commands to View Files with Patterns in Linux Mint and –help Flags for Any Command | Full Guide
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awk BASH Command in Linux Mint for Bioinformatics and Data Science | Data Manipulation Made Easy
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sed BASH Command in Linux for Data Science and Bioinformatics | Text Processing Made Easy
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Terminal Settings in Linux Mint for Bold and Zoomed-In Font Size and Style
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06: Zoom Meetings to know everyone
Zoom Meeting No. 1
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07: File Formats
Important File Formats for Linux | CSV, TSV, TXT, FASTQ, FASTQ.GZ, FASTA, fna, faa Explained
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08: VScode installation
VScode installation and other software installation methods in Linux mint
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09: Conda environments for Bioinformatics
Conda, Mamba & Python Environments for Bioinformatics and Data Science | Manage Packages Like a Pro
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Install Miniconda in Linux Mint | Step-by-Step Guide for Bioinformatics & Data Science
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Install Mamba in Linux Mint | Faster Alternative to Conda for Bioinformatics & Data Science
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Create Conda Environments in Linux | Comprehensive Miniconda Guide for Bioinformatics & Data Science
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10: git and gitHub
Git & GitHub in Linux for Bioinformaticians | Version Control Made Easy
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11: R and RStudio
Install R and RStudio in Linux Using Command Line | Complete Guide for Data Science & Bioinformatics
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R Programming Crash Course (11 h 55 m) – Learn R with Dr Aammar Tufail | Urdu/Hindi #rwithaammar
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12: Linux Tool installation and use for Bioinformatics
Linux tips and updates about software use in bioinformatics
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Tools installation and use | grabseqs and sequences download from NCBI
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Download raw data from a manuscript from NCBI
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Downloading raw data using terminal and other commands
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Download completed in terminal with fasq.gz files having less space
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Metadata related to fastq files and csv file opening in libre office linux
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13: Sequencing Technologies
Seuencing Technologies
Reading
14: Quality Control of Short Reads
Quality control of short reads using fastqc and multiqc | understanding number of threads in Linux
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15: DNA and DNA sequencing
DNA and DNA Sequencing Technologies | Short Reads vs. Long Reads
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Important Guide about sequencing technology
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Sequencing workflow and fastq files | zipped vs. unzipped files
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Bases vs. Base pairs in genome sequencing
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16: Genes and Genome
Difference between Genes and Genomes
Reading
How big is a genome and how does it looks like?
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17: Prokaryotic vs. Eukaryotic Genomes as bioinformatician’s perspective
Prokaryotes or unicellular organisms
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Eukaryotes or Multicellular organisms
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Prokaryotes vs. Eukaryotes Major differences
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Prokaryotic genome structure
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How to calculate GC content in a genome?
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Eukaryotic genome structure | Exons vs. Introns
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Genome Size Comparison Prokaryotes vs. Eukaryotic genomes
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Prokaryotic genes vs. Eukaryotic Genes structures
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Why should you start learning from prokaryotic genomes? | Bioinformatics
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Resources and Databases for Prokaryotic & Eukaryotic Bioinformatics
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Tools for Prokaryotic vs. Eukaryotic Bioinformatics analysis
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Real Wold Application and Job Market | Prokaryotic vs. Eukaryotic Bioinformatics
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Complete Guide with Notes
Reading
Quizzes-01
Quizzes for Practice _ Bioinformatics ka chilla
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Quiz No. 1: Linux and Conda Quiz
Reading
Quiz No. 2: Prokaryotes, Eukaryotes, Genes, Genomes & Sequencing Technologies
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18: Marker Gene Analysis | 16S rRNA, 18S rRNA, ITS
16S rRNA gene and its importance for Microbial Ecology
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What is taxonomy?
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Levels of Taxonomy for Bacteria | Understanding Classification Theory with Examples
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18S rRNA and ITS for community analysis | Metabarcoding | Amplicon sequencing
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19: VScode, Git, GitHub, Markdown
Install and use VScode in Linux as editor and IDE with sync from your github
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VScode experties | files, folders, interface, and settings
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VScode extensions
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Version control systems for coding and git
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Git installation
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Git CheatSheet
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Git with terminal | local repository commands
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Git with VScode for local repository making and tracking changes
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hidden folder (.git ) and reseting repo
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Git and GitHub using VScode to sync and use online repo
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Git cloning online public repositories with three methods
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Complete Markdown Guide | 72 Minutes (Adapt to Linux lecture is in Windows)
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20: Whole Genome Sequencing (WGS) and Genome Assembly workflow | Bacteria/Archaea
Intro to whole genome sequencing and assembly
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Select the paper and bacterial strain for raw sequence RAW reads files
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Extract raw reads from NCBI SRA using grabseqs
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Genome assembly workflow summary so far
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raw reads and meta-data exploration
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Genome assembly example in bandage and IGB for Bacteroides fragilis NCTC9343 from NCBI
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Short reads only genome assembly workflow and plan
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Short reads only assembly quality control of short reads automation
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Short reads genomes assembly guide and limitations with repeat regions
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fastqc quality report reading
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fastp use for read processing and trimming
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SPAdes as short reads assembler
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SPAdes output files for short reads only assembly
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Read spades output files and folders to make sense
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CheckM2 for Genome assembly quality check - Installation to use Complete Guide
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Task to use QUAST for quality check of genomes by yourself
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QUAST for quality evaluation | QUAST Part-1/2
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QUAST expert mode run for genome quality evaluation | QUAST Part-2/2
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QUAST outputs and reading results
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use BUSCO as genome assembly quality check | A-Z
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Types of genome assemblies based on quality metrics
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Tips to improve genome assembly quality
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Genome annotation with Prokka and Bakta
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Installation and analysis script is available on github
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Hybrid Genome Assembly Guide from Raw Reads (short + Long) | A- Z
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Results of Unicycler for Hybrid Genome Assembly
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Find plasmids in a genome using plassembler
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AMR genes and mobile genetic elements | ABRicate and geNomad
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geNomad to find mobile genetic elements inside a genome | A-Z
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Whole Genome Sequencing and Genome assembly | Summary
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Tips to run script step by step for whole genome assembly
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Genome taxonomy and script
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Genome Taxonomy and database use GTDB-TK | A-Z guide
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Average Nucleotide Identity ANI score and cutoffs for novel species
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Reading Materials
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Quiz Whole Genome Sequencing and Assembly
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CompareM2 for genome assembly comparison | Big Pipeline
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21: RNAseq/Transcriptomics | for Prokayotes (Bacteria and Archaea)
01-RNAseq or Transcriptomics | Introduction and plan
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02-RNAseq task for students --- Must learn from this task
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03-RNAseq sessions and tips for learning
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04-Central dogma and Transcriptomics
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05-Isolate vs. Community of organisms
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06-Cultured vs. Uncultured Organisms
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07-What is a genome?
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08-Key Aspects of a Genome important for Omics
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09-Omics Techniques to learn as a Bioinformatics and Transcriptomics
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10-RNAseq steps, history and tools | RNAseq vs. Riboseq
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11-Task for Single Cell Transcriptomics | What do you think?
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12-Types and Methods of Transcriptomics Analysis
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13-Bulk RNAseq example in detail
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14-Steps involved in RNAseq experiments
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15-Study Design in RNAseq experiment Step-1
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16-Library preparation and sequencing Step-2
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17-Deeper sequencing or More replicates for RNAseq experiment
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18-Read length for sequencing for illumna
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19-Single End vs. Paired End Reads from Illumina
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20-Two important costs for RNAseq Experiments
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21-Sequencing short reads but which Illumna sequencing should we go for
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22-Learning short reads and long reads sequencing Illumina NanoPore PacBio
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23-Data output of sequencing machines | What happens after sequencing?
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24-Understand FASTQ file and Quality Score (phred score)
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25-FASTA file format vs. FASTQ
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26-Important file formats in OMICS | Genomics and other OMICS
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27-RNAseq workflow for Bioinformatics
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28-RNAseq pipelines for Transcriptomics analysis
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29-READemption RNAseq pipeline installation step by step guide
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30-Complete RNAseq Analysis A-to-Z Project for Salmonella sp.
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31-Task for RNAseq analysis for Students
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32-Handling errors for installations and run for READemption
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33-Methods to prevent errors for READemption
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34-READemption scripts are online on github
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35-Read count & Normalization for RNAseq
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36-RPKM FPKM TPM and Log2FoldChange in RNAseq
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37-READemption Output and results of RNAseq for interpretation
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38-DESeq output files reading and understanding
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39-Save your data first and then work on it
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40-READemption use for future analysis
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41-RNAseq analysis on a publication data for Archaea
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42-Complete RNAseq run for a Published dataset with Reademption | Started the Analysis
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43-Task for Students
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44-Pipeline successfully worked for the analysis
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45-Paper Output to read and link with Paper Outputs of RNAseq analysis
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46-IGB to read coverage files for each RNAseq outputs
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47-Docker with DockerHub for any bioinformatics tool
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48-Docker uninstallation issue and bugs
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49-Google Antigravity for Bioinformaticians and RNAseq + Docker
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50-Install Docker for Bioinformatics Tools
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51-Use docker for RNAseq analysis with READemption
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52-Five step guide for Docker containers use for RNAseq analysis
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53-RNAseq analysis for Paired-end reads with three conditions
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54-RNAseq analysis for this project and paper with samples and paired-end reads
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55-genome fasta and gff files for the sample Organisms
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56-Download raw reads for the sample paper for paired end reads
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57-Method No. 1 for RNAseq analysis for Paired-end reads
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58-Method No. 1 for paired-end reads with analysis example
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59-Method No. 2 for RNAseq analysis for Paired-end reads
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60-Method No. 2 for RNAseq analysis for Paired-end reads
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61-RNAseq analysis results for Merged reads Method No. 2
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62-Method No. 3 for RNAseq analysis for Paired-end reads
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63-rRNAs are bad for RNAseq analysis, really?
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64-Publication ready plots for RNAseq analysis outputs from READemption
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65-Task for Students for RNA analysis from a Paper
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66-RNAseq visualization Application for READemption output
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67-Functional Enrichment Analysis Application is ready
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68-Application deployment on streamlit cloud
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69-RNAseq course completed
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22a: Pangenomics
01-Introduction to Pangenomics
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02 -Tools and Pipelines for Pangenomics analysis for prokaryotes
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03 -Task for Pangenomcis run Panaroo analysis
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04-Pangenomics Workflow and the importance of generating pangenomes
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05-Core vs. Accessory Pangenomes
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06 -Pangenomics key concepts
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07-PanExplorer for Pangenome Analysis
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08-PanExplorer results and report reading for manuscripts
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09-Panaroo Pipeline run for Pangenome Analysis (Part-1)
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10-Panaroo Pipeline run for Pangenome Analysis (Part-2)
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11-Panaroo Results and understanding of outputs
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12-Cytoscape for network visualization of pangenome
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13-Task to run Anvio workflow for Pangenome analysis
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14-Data Visualization for Panaroo Outputs with automatic script and github repo for scripts
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22b: Anvio for Pangenomics
01-Installation of Anvio Pipeline | Anvio for Pangenomics
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02-Steps to perform Pangenome analysis using ANVIO pipeline
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03-Hands on Pangenome Analysis using Anvio with Real Genomes (Part-1/2)
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04-Hands on Pangenome Analysis using Anvio with Real Genomes (Part-2/2)
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05 -Task for students to do Pangenome analysis
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06-Graphical User Interface of ANVIO Pangenome Main Menu
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07-Anvio pangenome BINs and Options
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08-Dendograms and layes in Anvio pangenome
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09-Search function of Anvio and layers in Anvio Pangenome
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10-Legends in Anvio Pangenome
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11-Anvio ANI using pyANI and layers on Pangenome
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12 -Split pangenome parts from main pangenome
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13-Task for Students Anvio Pangenome (Part-1)
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14-Task for Students Anvio Pangenome (Part-2)
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15-Ideas for Pangenome analysis
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16-Important key ideas for Pangenome manuscripts
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17-Pangenomics strategies for complete studies and papers
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18-Step 1: QC before pangenomics
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19-Step 2: Define biological questions clearly for pangenomics
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20-Step 3: Inspect core vs. Accessory vs. Sigleton in pangenome
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21-Step 4: Build a phylogenomics view of pangenome
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22-Step 5: Functional Enrichment Analysis and Annotation
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23-Step 6: Identify clade specific gene clusters in pangenome
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24-Step 7: Explore Genome organization and synteny
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25-Step 8: Check for Mobile Genetic Elements
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26-Step 9: Test pangenome Openness
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27-Step 10: Link Meta data to presence absence matrix of genes
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28-Step 11: Pangenome and ANI score
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29-Step 12: Look for Evidence of Horizontal gene transfer
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30-Step 13, 14, 15: Analysis to results reporting
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31-Step 1 to 15: Summary of Strategies for Pangenome Analysis and Reporting in papers
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32-Practical Guide for Pangenome Analysis in guided steps
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33-Most common mistakes in Pangenome analysis and Strategies to overcome
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34-Task for Students for ANVIO Pangenomics analysis
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23: CAZyme (Carbohydrate Active Enzymes) and PULs (Polysaccharides Utilization Loci) Analysis
01-What are CAZymes?
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02-Types of CAZymes based on functions
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03-Why CAZymes are important for biologists?
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04-Steps to do CAZyme analysis and tools
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05-Installation of dbcan for CAZyme analysis
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06-CAZyme analysis complete tutorial on Linux
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07-CAZyme Analysis figure ideas for Publications
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08-CAZyme and PULs analysis with two different genomes and plotting the results for Manuscript
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24: Secretion Systems in Bacteria (Type-I to Type-VI and Type-IX)
01-Genomes to Pangenomes and AMR genes plus much more
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02-Secretion systems in Bacteria introduction
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03-T1SS to T6SS and T9SS in details
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04-Bioinformatics tools for secretion systems analysis and detection
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05-Research projects based on Secretion systems in Bacteria
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06-Linux for Secretion systems with MacSyFinder and TXSScan complete guide
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07-Task for students for Secretion systems
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08-TFFscan | CONJscan | CasFinder systems in a genome
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25: CRISPR_Cas, CONJscan and TFFscan systems in Bacterial Genome
TFFscan | CONJscan | CasFinder systems in a genome
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26: Amplicon Sequencing (Microbial Ecology)
01-Microbial Ecology and 16s rRNA sequence analysis
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02-16S rRNA gene and Amplicon sequencing analysis using QIIME2
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03-QIIME2 installation in linux with conda giving errors
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04-Installation of QIIME2 using conda and mamba in linux (Working fine)
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05-Task for Students
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06-QIIME2 analysis of real data as an example
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07-Metadata to visualization as QIIME2 artifact
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08-Jupyter notebooks are much better than CLI for QIIME2 analysis
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09-Importing data in QIIME2 to use for analysis
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10-Demultiplexing the data in QIIME2 for amplicon sequencing
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11-Summary of next steps
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12-DADA2 for denoising the samples
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13-Deblur for denoising the samples
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14-Feature Tables summary and representative sequences
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15-Generate Phylogenetic trees after aligning the data
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16-How to view phylogenetic trees in iOTL?
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17-Assignment alert before next lecture
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18-Alpha vs. Beta diversity introduction and need in Amplicon sequencing
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19-Alpha diversity Richness vs. Evenness
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20-Alpha diversity Metrics and Methods
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21-List of Alpha diversity Metrics in Qiime2
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22-Beta diversity methods and metrics
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23-Assignment or task alert
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24-PCA | Principal Component Analysis | Theory
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25-PCA | Principal Component Analysis | Case Study in Python
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26-PCA vs. PCoA analysis for Beta-diversity analaysis
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27-Alpha- and Beta-Diversity Core Metrics in one code with optimization with group significances
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28-Assignment Alert | Very important one
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29-Group Significance in Alpha-diversity continuous variables with metadata
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30-PERMANOVA Analysis for Beta-diversity metrics and Meta-data using QIIME2
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31-PCoA plots to view and understand beta diversity using QIIME2
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32-Alpha-rarefaction plots and ASVs with sequencing depth
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33-Taxonomic analysis using Machine Learning
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34-Taxonomy in Amplicon sequencing is an important step
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35-Taxonomy analysis using QIIME2 using classifier training with ML
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36-Taxonomy analysis in QIIME2 using pre-trained SILVA database classifier
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37-Differential Abundance analysis using ANCOM-BC in QIIME2
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38-Next steps in Amplicon Sequencing analysis using QIIME2
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39-Complete A-Z Guided Tutorial of Microbial Ecology Analysis using QIIME2 for Amplicon sequencing
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40-Impact of Amplicon sequencing analysis and figure interpretation
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41-16S vs. 18S vs. ITS analysis
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42-Tools for Amplicon sequence analysis
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43-Amplicon sequence analysis from a published article
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44-Download raw data based on publication
Video - 00:19:20 mins
45-Code is available in this lesson
Video - 00:00:15 mins
46-QIIME2 for ITS and Github copilot
Video - 00:16:45 mins
47-Amplicon sequence with ITS completed
Video - 00:03:47 mins
27-Metagenomics A-Z
01-Metagenomics | introduction for beginners
Video - 00:20:56 mins
02-Key Terminologies and Analysis pipeline in Metagenomics
Video - 00:06:10 mins
03-QIIME2 MOSHPIT installation and tools for metagenomics
Video - 00:16:08 mins
04-Assignment for Students
Video - 00:02:28 mins
05-Understanding Metagenomics Made Easy
Video - 00:06:10 mins
06-Metagenomics with MOSHPIT QIIME2 workflow understanding
Video - 00:14:12 mins
07-Raw Reads to Contigs building
Video - 00:10:27 mins
08-Understanding De Bruijn Graphs in the Best Possible Way
Video - 00:22:28 mins
09-Assembly QC
Video - 00:02:07 mins
10-Read Mapping for Metagenomics
Video - 00:03:43 mins
11-Contig Binning to MAGs reconstruction
Video - 00:06:26 mins
12-MAGs QC and MAGs filtering
Video - 00:01:21 mins
13-MAGs Dereplication
Video - 00:03:04 mins
14-Taxonomic Classification
Video - 00:02:00 mins
15-MAGs abundance estimation
Video - 00:02:43 mins
16-Taxa Barplots for Taxa understanding
Video - 00:00:31 mins
17-Summary, common mistakes and Conclusion
Video - 00:07:13 mins
18-Hands on Tutorial for MAGs reconstruction using QIIME2 MOSHPIT
Video - 00:29:09 mins
19-Assignment for Students
Video - 00:00:42 mins
20-Exploring results of MAG reconstruction tutorial and what we actually need for paper
Video - 00:16:25 mins
21-Cocoa Fermentation tutorial understanding and start
Video - 00:04:02 mins
22-COCOA Fermentation Tutorial Understanding of Data and treatments
Video - 00:06:02 mins
23-Download raw data with ENA using SRR list for cocoa fermentation if we need to use RAW reads
Video - 00:09:24 mins
24-Anvio for metagenomics Installation of Anvio Pipeline
Video - 00:28:40 mins
25-Anvio for Metagenomics and shortreads QC
Video - 00:30:06 mins
26-Parallel computation and Anvio for Metagenomics
Video - 00:23:44 mins
27-QC reports of reads
Video - 00:02:14 mins
28-How did I select Samples subset?
Video - 00:01:44 mins
29-Assignment Task for Students
Video - 00:01:22 mins
30-Scripts used till now for Metagenomics and Data Retrieval
Reading
31-Megahit Co-Assembly is ready to view and check
Video - 00:10:11 mins
32-QC Reports and MultiQC Reports
Video - 00:04:57 mins
33-Co-assembly QC with Metaquast and graph with Bandage
Video - 00:11:36 mins
34-Metaquast error due to insufficient RAM
Video - 00:04:42 mins
35-QUAST and MetaQUAST worked with fewer references
Video - 00:05:55 mins
36-Optimizing Metaquast: RAM issues killed the process
Video - 00:01:05 mins
37-Metaquast is almost working properly
Video - 00:01:14 mins
38-Metaquast worked fine and now we can see results
Video - 00:01:14 mins
39-Anvio reformat fasta files of contigs before mapping
Video - 00:03:36 mins
40-Reformatting and Indexing done Mapping started with parallel computation
Video - 00:03:39 mins
41-Mapping done and results are ready
Video - 00:01:18 mins
42-sorting and indexing of bam files
Video - 00:02:32 mins
43-sorting completed and results are here
Video - 00:00:45 mins
44-Creating ANVIO compatible database of contigs
Video - 00:01:06 mins
45-Run HMMs on contigs with results
Video - 00:02:40 mins
46-Display contigs stats in iteractive view of Anvio
Video - 00:02:41 mins
47-Profiling of all samples using Anvi'o
Video - 00:08:31 mins
48-Profiling completed and results are here
Video - 00:02:23 mins
49-Merge all profiles using this command
Video - 00:02:33 mins
50-Merging completed but with warnings
Video - 00:01:38 mins
51-What Merging Profiles Means?
Video - 00:00:36 mins
52-Binning and binning tools available for metagenomics and their installation outside Anvio env
Video - 00:03:51 mins
53-Prepare for binning tools outside Anvio
Video - 00:02:55 mins
54-Metabat2 binning algorithm and its outputs
Video - 00:01:34 mins
55-Concoct as a binning algorithm: Script and output
Video - 00:02:11 mins
56-MaxBin2 binning algorithm script and output comparison
Video - 00:03:04 mins
57-Prepare outputs of all three binning algorithms for DAS Tool
Video - 00:08:22 mins
58-DAS Tools to combine outputs of all three script and runtime
Video - 00:05:43 mins
59-DAS tool output and files
Video - 00:02:11 mins
60-DAS Tools output import in Anvio and summary details of final Bins
Video - 00:17:54 mins
61-MAG quality Estimation after binning
Video - 00:07:29 mins
62-All binning tools and MAGs quality estimation summaries
Video - 00:14:41 mins
63-Taxonomic classification of MAGs using Anvio SCG Taxonomy Script is provided
Video - 00:06:10 mins
64-Data visualization of Taxonomy
Video - 00:01:35 mins
65-Data Visualization and publication ready figures from MAGs
Video - 00:08:29 mins
66-Assign Taxonomy to Sample Metadata
Video - 00:03:31 mins
67-Selection of High Quality HQ MAGs
Video - 00:03:36 mins
68-Export fasta files of each MAG based on Quality and binning tool
Video - 00:02:51 mins
69-Run Functional Annotation and Taxonomy for contigs to know who is there and what they are doing
Video - 00:03:42 mins
70-We have learned so far these topics
Video - 00:03:38 mins
71-PC management guide for Bioinformaticians using threads cores and ram with SSD
Video - 00:22:14 mins
72-Anvi’o tutorials are important for everyone for OMICs
Video - 00:03:17 mins
73-Simple read recruitment exercise using Anvio pipeline
Video - 00:44:50 mins
74-Assignment task for students
Video - 00:1:20 mins
75-Further tips and the use of the MetaWRAP pipeline for metagenomics analysis
Video - 00:05:52 mins
76-Further analysis of MAGs are similar to WGS analysis
Video - 00:22:52 mins
77-Limitation of doing metagenomics analysis in Pakistan or abroad
Video - 00:09:45 mins
78-Assignment for students
Video - 00:00:48 mins
79-What are we learning from now on
Video - 00:02:07 mins
28-Viromics
01-Viromics Introduction
Video - 00:09:17 mins
02-Types of Virus genomes
Video - 00:05:02 mins
03-Virus's genomes vs. Bacterial genomes
Video - 00:05:32 mins
04-Examples of Viral Genome Structure
Video - 00:02:45 mins
05-Baltimore classificationof viruses
Video - 00:04:04 mins
06-Lytic vs. lysogenic viruses
Video - 00:04:04 mins
07-Viromes across environments
Video - 00:06:21 mins
08-Viral Dark Matter and Classification
Video - 00:02:06 mins
09-Fundamentals of Viromics
Video - 00:06:27 mins
10-Experimental design for Viromics studies
Video - 00:16:53 mins
11-Studies about Viromics and latest papers to study
Video - 00:09:38 mins
12-RNA vs. DNA extraction kits for Viruses
Video - 00:01:32 mins
13-Assignment----Research Papers on Viromics to Read
Video - 00:01:21 mins
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