20 May 2013

Aphaenogaster, Medicago, and Bradyrhizobium

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Monday bioinformatics

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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