This course is a 1 unit optional laboratory counterpart to “Genomics” (HMGP 7620) offered in the School of Medicine at UC Denver for Spring 2010.  The objective of this unit will be to give students with little programming or Linux/UNIX proficiency enough background and hands-on experience to be able to: write simple scripts to obtain, reformat, and process large genomic data sets, perform basic data manipulation including sequence alignment, mapping, assembly, and homology-based search, and to extract meaningful information from pattens of intra- and inter-specific genomic variation using phylogenetic methods, simulation, and advanced statistical techniques. 

The workshop is now full, but will hopefully be offered again sometime in the near future.

Please note, assignments should be emailed to:

assignments@jasondk.org

Week 1 - Introduction to UNIX/Linux and Perl

1. -Jianbin’s slides are here
   

2. -For your use at home, VMWare Player can be downloaded from here
   

3. -Ubuntu Linux can be downloaded here
   

1. -The reading for next week, “Having a BLAST with bioinformatics (and avoiding BLASTphemy)”,  can be downloaded here
   

Week 2 - Genome browsers and BLAST

1. -Jason’s slides for this week are here (printable B&W here).
   

2. -(The programming assignment is in the lecture notes.)
   

3. -The genome browser data retrieval assignment is here.
   

1. -Optional Genome browser background and tutorial materials can be downloaded here.
   

Week 3 - Dealing with next-gen sequence data

1. -Jason’s slides for this week are here (printable B&W here).
   

2. -The programming assignments are integrated with the data analysis assignment this week (see slides).
   

1. -Velvet, the short read assembler, can be downloaded here.  The manual is here.
   

2. -The short read simulator script that you’ll need to modify is here.
   

Week 4 - Next-gen sequencing (continued) and Genome browsers advanced topics

1. -Jason’s slides for this week are here (printable B&W here).
   

2. -This week is mainly a continuation of last week’s integrated assignment. 
   

3. -In addition, we will be BLASTing our contigs from Velvet back against our template regions, and visualizing the BLAST results on the UCSC Genome Browser.
   

1. -A bonus assignment has also been prepared, using an error-prone short read simulator (script is here).
   

2. -The simple BLAST output to BED converter is here.
   

1. -A number of very simple practice programming exercises will also be posted shortly.  One problem set will be due every week from now on.
   

Week 5 - Introduction to R

1. -Jason’s slides for this week are here (printable B&W here).
   

2. -The practice problem set questions (mini programming assignment) are here.
   

1. -The main R website.
   

2. -Some background reading on R, if you are so inclined, is here.
   

3. -The exampleData.txt file referred to in the R notes.