2012 October 3

==Matters arising==
===Major projects for course===
#Your favorite gene-- Your assigned work is done, but you may continue to work on this article as you wish.
#Genetic study (mutations and phenotypes)
#Genomic study (whole genome analysis of DNA and its RNA and protein products)
#Metagenomic study
==DNA sequencing methods==
===JMB: Short presentation on bias and errors in DNA sequencing===
===Student presentations and discussions of sequencing methods===
===Video Resources on DNA sequencing===
Eric Lander on DNA sequencing. 2012. 18 min video of lecture describing basic Sanger DNA sequencing to undergraduates, from MIT Open Courseware. Eric is the director of the Broad Institute, and quite possibly the smartest person I have ever met (JMB).
Jon Eisen on DNA Sequencing. 2012. 70 min video that provides an excellent overview of high-throughput DNA sequencing methods, including their relative advantages and limitations. Jon is a professor at University of California, Davis.
===Publications on DNA sequencing===
Mardis, E.R. (2008). Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9, 387-402.
Metzker, M.L. (2010). Sequencing technologies - the next generation. Nat Rev Genet 11, 31-46.
==Chapter 3: Mapping, sequencing, annotation and databases==
#Chapter content, concepts and issues
#Exercises, problems and weblems
==Class Notes==
DNAseq: Problems, errors, bias, and limitations
*Errors: There are technical errors that can be delt with via advances in the accuracy of technology.
**Small-scale errors: Wrong base call at particular positions. Normally fixed through resequencing or multiple repeats within the method.
**Large-scale/assembly errors: Correct small sequences put together in the wrong order. A larger read length = fewer errors, ie. less ambiguity in resequecing.
**Both of the above are technical errors that can be dealt with. Also completing test runs helps researchers "know" the machine and avoid these errors.
*Systematic Bias
**The more required sample preparation and processing steps, the more systematic errors (goes against scientific parsimony). An example of this is that if there is one sequence that does not amplify well, it may be under represented while resequencing. DNA can fold on itself and not be sequenced.
There are 2 'Holy Grail' methods of sequencing that are closer to being useful. These methods utelize direct copies of long read sequences and does not require amplification:
*Pacific Biosystems Method
*Oxford, Nanopore method