20 May 2013
Aphaenogaster, Medicago, and BradyrhizobiumNext post Previous post
Google scholar alert turned up a paper An Illustrated Angiosperm Flora of Cerrado and Riparian Forest, Sao Carlos, Brazil with location information for some Chamaecrista species in Brazil.
CheckList looks like a great journal - free to publish, open-access for species distribution lists.
Continuing to work on script for genomic prediction by cross-validation (see above…modifying in place). Found that gcta v1.04 crashed when I tried to calculated SNP effects, but after downloading newest version (v1.13) it worked fine.
Use STAR for alignment of reads to transcriptome
Downloaded Pogo RNAseq data to antlab to run with Velvet/Oases.
Back to assembly. Mapping to B. japonicum reference resulted in very little assembly, probably too diverged, so focus on de novo assembly using velvet. Last results using velvet about a month ago
MUCH belatedly discovered a
-v option for submitting batch jobs to MSI that allows passing a variables list
qsub 04-VelvetOptimiser.pbs -v B-elkanii-genomes/velvet1/VelOpt,/home/tiffinp/stanton1/B-elkanii-genomes/fastq-shuffled/IC1_shuffled.fastq
Signed up on RAST for annotation
New website with jekyll information
While thinking about Aphaenofest, found amazing resource for presentations using reveal.js. Has a very nice web interface. Examples and links to alternatives at this post
Seems to combine best functionality of WYSIWYG design with text-based editing and reproducibility!
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