The Genomic Analyses Club - Page 2

This week, we'll discuss a new paper by Feng et al. (2014) that shows that for some toothed and baleen whales, all food just tastes salty. Again, all CELS members are very welcome to join!

We will be discussing a recent paper by Roesti et al. (2014) which uses simulations and stickleback data to test for patterns of adaptive divergence in the genome. We particularly invite participants of the CELS endringsmiljø!

We will discuss Fang et al. 2013 Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing (Nature Biotechnology 30: 1232-1239).

We will discuss sequencing technologies for transcriptome dat. We will focus on the downstream analyses and use the Pacbio human transcriptome paper as a starting point for our meeting (Sharon et al. 2013 A single-molecule long-read survey of the human transcriptome. Nature Biotechnology 31: 1009-1014).

Lex Nederbragt will present visualisations in the demonstrate the IGV Genome Browser from the Broad Institute, using two validated assemblies. 

We will discuss quality control! The following paper will be a starting point for our discussion: Guo et al. 2013 Three stage quality control strategies for DNA resequencing data (Briefings in Bioinformatics 2013: online early)

We'll have a brainstorm on SNP calling from whole genome sequencing data. I'll briefly describe the pipeline I've run up to now, which is mostly preceding actual SNP calling, and then want to focus the discussion on how to get a high quality SNP dataset from low coverage resequencing - i.e. how to call SNPs, what filtering criteria to use to distinguish high from low quality SNPs, and how this may vary depending on the subsequent analyses we want to do with our SNP data. This will really be a brainstorm, an open discussion, all ideas welcome. If you would like to read up a bit beforehand, I can recommend the guide form the Broad Institute which has been one of my guidelines along the way (http://www.broadinstitute.org/gatk/guide/best-practices).

We will discuss Opazo et al. 2013 Whole-Genome Duplication and the Functional Diversification of Teleost Fish Hemoglobins (MBE 30: 140-153).

Note different time and day!

Discussion of Linnenbrink et al. 2013 The role of biogeography in shaping diversity of the intestinal microbiota in house mice (Molecular Ecology 22: 1904-1916).

This week at TGAC we have the pleasure to listen to Geir Kjetil Sandve and Sveinung Gundersen from IFI, who will give a presentation about "Doing bioinformatics more efficiently and reproducible with the Galaxy platform"

Discussion on the program SNAPP (SNP and AFLP package for Phylogenetic Analyses) and the associated paper by Bryant et al. 2013 Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis (MBE 29: 1917-1932).

Discussion of Hufford et al. 2012 Comparative population genomics of maize domestication and improvement (Nature Genetics 44: 808-811).

Discussion on two (!) papers: (i) Le & Durbin 2011 (Genome Research 21:952-960) and (ii) Roesti et al. 2012 (BMC Evolutionary Biology 21:94).