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H3ABioNet SOPs
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Organization
Genomic Analyses
Human variant calling
Genome Wide Association Studies
RNA Sequencing data analysis
16S Diversity analysis
Contributing
Technical Guide
Language & Style
Feedback
RNA-Seq SOP 4.0
Introduction
Introduction
Glossary of associated terms and jargon
Overall procedure
Phase I. preprocessing raw reads
Quality check
Adaptor and Quality Trimming
Quality recheck
Phase II. Counting features
P1- Gene/Transcript level counts
P2- Gene/Transcript level counts
P1- Cout generation
P2- Cout generation
P1- Collecting & tabulating stats
P2- Collecting & tabulating stats
Phase III. Statistical analysis
Outlier/ Batch detection
Removal of low count genes and Normalization
Differential expression statistics
Working with Galaxy
Note about Galaxy
H3ABioNet Accreditation exercise
Practice dataset
Reproducible research
General questions
Analysis-specific questions
RNA-Seq data processing and gene expression analysis
QC and outlier/batch detection
→
Low-count genes removal & normalization
→
Differential expression Statistics
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Phase 3: Statistical analysis
Bibliography
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