This course will meet in 2 hour blocks three times per week all semester.
Week
1 Introduction to
genomes
2
Prepare Samples for
Sequencing
Introduction to reading
journal articles
3
Assembly preparation
4
Assembly & Annotation
practice
5
Assembly & Annotation
6
Annotation
7
Annotatoin U&
Analysis
8
Spring Break
Topic/Activity
Examine online genomic data, gene structure, discuss
where this information comes from, how it is used, etc.
Prepare to build our own genome! (pre-modules)
Primer on genomic DNA isolation
Isolate Genomic DNA & assess quality
Journal Club
Challenges & theory – assembly exercises on paper
Linux access & tutorial; file types
Practice day 1– Data Quality and Error Correction
Practice day 2 – Assembly using SOAPdenovo2 walk
them through beginning, they finish and compare
results 1X, and 10X
Practice day 3 – Repeat masking
Practice day 4 – Whole genome analysis
Data Quality and Error Correction
Assembly using SOAPdenovo2 (one run? or many?)
Repeat masking
Whole genome analysis
Comparative Genomics using CoGe
Stacks SNP finding
Stacks
R studio
Homework
Extract info from Wormbase & UCSC Genome Browser
Journal Article: introducing genomics
More Linux at home following a video of Dave’s design
Journal Article: best practices for assembly, plan
assembly settings
Practice 100X
Can they assemble a simple genome?
Journal Article
9 Project proposals
More detailed annotations?
Research Questions & Literature Search
Literature workshop
10 Projects
Project proposal development
Begin projects
11 Projects
Generate and analyze project data
12 Projects
Interpret and contextualize results
13
14
15
16
Write Manuscript
Write Manuscript
Draft Manuscripts
Work on Presentations
Deliver Presentations
Final Manuscript
annotations ongoing?
formulate a good research question
peeer review project proposals
instructor review project proposals
short annotated bibliography
work on projects in class and at home
write results and begin discussion
generate figures
tie aspects of manuscript together
due at final exam time
Access their data set – Technical Challenge: assemble in one run, or each student assemble?
Discuss assembly results, N50 score; can compare to Andre’s assembly
Phylogeny Exercise ?
Annotation – 2 weeks in class, more at home – 50 genes/student in the end?
Additional Modules: simple programming in Panther (so they know how some of the software they use works) (Dave can do this ‘easily’)