#Schedule

This is a multi-day course with hands-on bioinformatics analyses accompanied with discussions of fundamental physiological processes, specific case studies, and underlying laboratory techniques. The general objective of this course is to provide participants with core computing skills and experience with genomic datasets.   

One primary case study will be the examination of novel transcriptome datasets from reproductive tissue from two bivalves. The underlying goal of the week long course is to produce a cohesive analysis product. 

##Day 1
- Set-up computing environments for bioinformatics analysis and learn basic unix commands.    
- Use version control for effective documentation of analyses, backup, and collaboration

1) **AM Lecture**:  Roberts _Introduction_     
2) Getting comfortable with text and command-line. Open [shell.md](https://github.com/sr320/course-btea/blob/master/day-1/00-shell.md). For this everyone will jump right in with [a bash shell](https://github.com/sr320/course-btea/wiki/Before-you-arrive#the-bash-shell).     
3) [Markdown](https://github.com/sr320/course-btea/wiki/Before-you-arrive#markdown-editors) Lets get out of the shell for a bit to learn markdown and why it is valuable (spoiler: version control).    
4) [Version control](http://swcarpentry.github.io/git-novice/10-open.html) - Github        
5) [Jupyter](https://jupyter.org/)        
6) [SageMathCloud](https://cloud.sagemath.com/)             
7) **Activity** - Notebooks set-up _Describe transcriptome_  (Show how generated)         
	- Assemble transcriptomes - maybe iPlant, Galaxy.          
	- _Product_ - publish notebook post links on wiki by end of day!!        
	- ITP -  Start blast

---

##Day 2
- Characterize and annotate novel transcriptomes 

1) **AM Lecture**:  Vadopalas _Bivalve Reproduction: a tale of two species_            
2) Blast          
3) Compare to full genome (maybe start day before)        
4) Predicted Proteins      
6) **Activity**       

---

##Day 3
- Identify differentially expressed genes   

1) **AM Lecture**:  Vadopalas _Ecological and hatchery perspective on reproduction_        
1) DESeq - - RNASeq Heat Shock!- gonads        
2) Sex specific genes       
2) Enrichment analysis         
3) Proteomics??? (might not have time)         
4 ) mini project - Relationship of dm-TE and DE (todoist)       

Activity 

---

##Day 4
- Assess epigenetic variation in relation to genomic feature

1) **AM Lecture**:  Roberts _Epigenetics: this changes everything_    
1) In silico anlaysis        
Do corals
then new transcriptomes          
2) Bisulfite data -