Bioinformatics for Beginners 2022
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Bioinformatics for Beginners 2022
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Module1 - Unix/Biowulf
Module1 - Unix/Biowulf
Lesson 1: Introduction to Unix and the Shell
Lesson 2: Navigating file systems with Unix
Lesson 3: Introduction to Biowulf
Lesson 4: Useful Unix
Lesson 5: Working on Biowulf
Lesson 6: Downloading data from the SRA
Lesson 7: Downloading the RNA-Seq Data and Dataset Overview
Introduction to RNASeq
Introduction to RNASeq
RNA-SEQ Overview
Generating the Data
Data Analysis Overview
Data Analysis
Alignment
Quantitation
Differential Expression
Visualization
Resources
Module 2 - RNA sequencing
Module 2 - RNA sequencing
Lesson 8: Introduction to RNA sequencing
Lesson 9: Reference genomes and genome annotations used in RNA sequencing
Lesson 10: Introducing the FASTQ file and assessing sequencing data quality
Lesson 11: Merging FASTQ quality reports and data cleanup
Lesson 12: RNA sequencing review 1
Lesson 13: Aligning raw sequences to reference genome
Lesson 14: Visualizing alignment results
Lesson 15: Finding differentially expressed genes
Lesson 16: RNA sequencing review and classification based analysis
Module 3 - Pathway analysis and course review
Module 3 - Pathway analysis and course review
Gene ontology and pathway analysis
Gene ontology and pathway analysis: PowerPoint slides
Database for Annotation, Visualization and Integrated Discovery (DAVID) - an overview
Introduction to Qiagen Ingenuity Pathway Analysis
Course Wrap-up
Help Sessions
Help Sessions
Lesson 2 Practice
Lesson 4 Practice
Lesson 5 Practice
Lesson 6 Practice
Lesson 7 Practice
Lesson 9 Practice
Lesson 10 Practice
Lesson 11 Practice
Lesson 12 Practice
Lesson 13 Practice
Lesson 14 Practice
Lesson 15 Practice
Lesson 16 Practice
Database for Annotation, Visualization and Integrated Discovery (DAVID) - practicing what we learned
References
References
References
Biostars Software Reference
Additional Resources
Additional Resources
Further readings and tutorials
Logging into Biowulf
Accessing the Biostar Handbook
Using the Biostars Module for Biowulf
Installing IGV
Installing IGV
Instructions for installing IGV
Questions and Answers
Questions and Answers
Questions and answers
Home copy
2020 Bioinformatics for Beginners Course using the Biostars Handbook