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RNA-Seq Analysis GCAT-SEEK Workshop Manual

Developed by Dr. Mark Peterson, this module provides an overview of the different types of RNA-Seq data analyses. It describes how to assess the quality of RNA-Seq data with FastQC, trim adapters and low quality data with Trimmomatic, read mapping with RSEM, differential expression analysis with DESeq, variant detection with VarScan, and de novo assembly with Trinity.


CourseSource Publication

Peterson, M.P., Malloy, J.T., Buonaccorsi, V.P., and Marden, J.H. 2015. Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching. CourseSource. https://doi.org/10.24918/cs.2015.14

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Metagenomics Workshop Manual

Developed by Dr. Regina Lamendella at Juniata College, this manual provides an overview of metagenomics sequencing and analysis. Module 1 describes the protocols for preparing microbial samples for Illumina sequencing, which includes preparation of the Illumina library, quantification of the pooled library with the Qubit fluorometer, and verification of the library quality with the Bioanalyzer. Module 2 illustrates how the QIIME 16S and Fungal ITS workflows can be used to analyze metagenomics datasets.

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Prokaryotic Genomics Lesson

Developed by Dr. Jeff Newman at Lycoming College, this lesson provides an introduction to the analysis of prokaryotic genomes. The lesson covers the protocols for isolating genomic DNA, de novo genome assembly, genome annotation using RAST, comparative genomics, microbial phylogenomics, and preparing the genome assemblies for GenBank submissions.

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GCAT-SEEK Eukaryotic Genomics Workshop Manual

Developed by Dr. Vince Buonaccorsi at Juniata College, the GCAT-SEEK Eukaryotic Genomics Workshop Manual consists of seven chapters that cover genome assembly, gene annotations, and variant calling:

  1. Genome assembly I: Quality control with FastQC and Trimmomatic
  2. Genome assembly II: Assembly size estimation and k-mer graphs
  3. Genome assembly III: Assembly algorithms
  4. Genome annotation with Maker I: Overview and repeat finding
  5. Genome annotation with Maker II: Whole genome analysis
  6. Whole genome annotation: Miscellaneous methods
  7. SNP calling and interpretation

CourseSource Publication

Buonaccorsi, V.P., Hamlin, D., Fowler, B., Sullivan, C., and Sickler, A. 2017. An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching. CourseSource. https://doi.org/10.24918/cs.2017.1

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Eukaryotic Genomics Pre-workshop Tutorial

This tutorial provides an overview of the key concepts that will be discussed during the GCAT-SEEK Eukaryotic Genomics Workshop:

  1. Linux tutorial: Some basics
  2. Genome Assembly: Overview & experimental design
  3. Genome annotation: Overview and manual annotation of a eukaryotic gene

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