13 September 2013
Aphaenogaster and transcriptomeNext post Previous post
Revisions to stats commentary…
Partial regression plots - use avPlot() in car package.
Line is a simple linear regression of residuals against residuals (as explained here)[https://stat.ethz.ch/pipermail/r-help/2007-February/125791.html]
Had to upgrade jekyll-pandoc plugin for pandoc to work.
Website for journal trolling: http://www.biosemantics.org/jane/
Editing scripts for transcriptome assembly using mason cluster. Standard no-frills velvet-oases assembly for comparison with Trinity and assembly using digital normalization
Installed raxML on antlab.
Edits to stats commentary
Helms-Cahan Lab meeting on how to make maps in R using Molecular Ecologist blog post
Running standard velvet assembly (no diginorm or merging reads) on mason where memory is not limiting.
Cloned github repository and including new (modified) scripts for full transcriptome assembly.
Full details on running jobs on mason here. I ran
qsub -l nodes=1:ppn=4,vmem=16gb -l walltime=06:00:00 -m e script
to specifify 1 node, 4 processors, 6 hours walltime and
-m e to have job summary mailed when job terminates.
‘a statistician being grumpy’ and some suggestions for solving problems with Bayesian statistics
Climate Cascade Meeting - ecological stoichiometry and Aphaenogaster
Received shipment of ApGXL ants from Clint:
Meeting with undergrad about research project involving DNA extraction
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