Oct. 8, 2012

Topic: Building phylogenetic trees

Discussion leader:  Sergio

Papers: Yang_Rannala_2012
            Zaspel_2012

Questions

Software: STARBEAST tutorial

Oct. 1, 2012

Topic: Genome assembly

Discussion leader:  Sandy

Readings: Haridas et al. 2011 + Supplementary data
                 Pop et al. 2009

Hands-on activity: Assembling 454 reads

1. Sign up for an account at iPlant
2. Login to the Discovery Environment
3. Navigate Apps>Public Applications>NGS>Assemblers
4. Open Newbler 2.6.0
5. Click the add button to add a .sff file of 454 reads
6. The file is under Community Data>iplantcollaborative>example_data>Newbler-2.6.0 and it is called FFGLB5S034.sff
7. Select "under 1h" for the run time under Run Options. Leave other defaults in place, launch and name the job.
8. You'll receive an email when the job has completed.
9. Go to your data folder under "analyses."
10. The assembled contigs will be under NewblerOutput>454AllContigs.fna.
11. Open this file to see the assembled genes. Some of the contigs have lower-case base letter - what do you think that means?
12. Paste a few of them into NCBI blast -- what species are they from?

Sept. 24, 2012

Topic: BLAST and its relatives

Discussion leader:  Christina

Readings and resources:
Nucleic acid alignment
Protein alignment
NCBI Blast Introduction
NCBI Blast charts

Optional readings:
Interview with Stephen Altschul
PSI-Blast paper
Delta-Blast paper

The first two readings (From Exploring Bioinformatics by St. Clair and Visick) provide a hands-on introduction to nucleic acid and protein Blasting. For next week, work through the examples and answer the questions provided.

The next two resources are basic Blast information from the NCBI website. The charts in the second link provide an overview of the many algorithms and databases available. We'll discuss them next time.

For the students who already have plenty of experience with Blast, check out the articles on PSI-blast and Delta-Blast, as well as the interview with one of the original Blast developers, Stephen Altschul. Think about how you might explain the differences among regular Blast, PSI-Blast and Delta-Blast to the group.

PS - You might find the "Taxonomy reports" (under other reports on the blast results page) helpful when looking at bacterial taxa for questions 5&6 of the nucleotide blast project.

Sept. 17, 2012

Topic: Quality filtering NGS data

Discussion leader:  Beth

Papers: Dohm et al. 2008
            Kircher et al. 2011

Discussion Questions

Software: FastQC

Datasets: Illumina reads 1, Illumina reads 2

Artifacts of random hexamer priming at 5' read ends

Note: Download and install FastQC on your computer. I'll be posting some Illumina read sets for you to quality-check, and we'll discuss the results on Monday. -Christina