[Coral-List] Methods in Ecological Genomic Analysis (MEGA2015)
matz at utexas.edu
Fri Feb 20 18:19:40 EST 2015
Dear colleagues -
we are pleased to announce the next year of our hands-on intensive workshops in ecological genomics. We will be teaching RAD and RNA-seq in the first two weeks of July. For now, please email us (all three of us) to indicate your interest (RAD, RNAseq, or both) and how likely you are to attend. Please respond by March 20, putting “MEGA2015” in the subject. First come - first served, classes are limited to 12 students each.
For additional general info, please see the last year's workshop’s website: http://www.bio.utexas.edu/research/matz_lab/matzlab/MEGA2014.html
Mikhail Matz, matz at utexas.edu
Groves Dixon, grovesdixon at gmail.com
Marie Strader, stradermarie at gmail.com
Methods in Ecological Genomics Analysis (MEGA) 2015
Intensive workshops for the uninitiated at the Mote Tropical Research Laboratory, Florida Keys
Instructor: Mikhail V. Matz, TAs: Groves Dixon and Marie Strader
Cost: $2,000 each, $3,700 both.
Class size: 12
Whole-genome genotyping with 2bRAD (June 30 – July 7)
2bRAD is the flavor of Restriction site Associated DNA genotyping methods. It is one of the easiest RADs to implement due to a very streamlined protocol, initially published in Nature Methods. The current protocol allows for simultaneous processing of hundreds of samples and removal of PCR duplicates prior to the analysis. Bioinformatics pipelines for 2bRAD offer genotyping quality assessment based on replicates and advanced variant call filtering adopted from the GATK pipeline used in human genetics. The class has four parts: (1) DNA isolation and library preparation (wet lab), (2) data processing and variant calling using LINUX-based high performance computing (HPC) cluster, (3) population genetic analysis including population structure and demographic modeling, and (4) population genomic analysis to identify loci under selection.
2bRAD paper: http://www.bio.utexas.edu/research/matz_lab/matzlab/Papers_files/wang12%202b-RAD.pdf
Global gene expression profiling with tag-based RNA-seq (July 7 – July 14)
Tag-based RNA-seq is a low-cost alternative ($50/sample) to conventional RNA-seq for quantifying the abundances of polyadenylated (protein-coding) transcripts. Low cost and ease of implementation allows for experimental designs involving extensive biological replication, leading to very high power and possibility to apply network-based approaches of gene expression analysis. The class has five parts: (1) RNA isolations and library preparation (wet lab), (2) initial data processing using LINUX-based high performance computing (HPC) cluster, (3) identifying differentially expressed genes using generalized linear models (DESeq2 package) and network approach (WGCNA package), (4) summarizing the data in terms of biological functions involved, (5) de novo assembly and annotation of transcriptomes.
Tag-based RNA-seq paper:
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