Monthly Archives: August 2015

Week 3 – NGS2015

Week 3 of NGS 2015 comes to a close. Discussion on what attendees and instructors have gained from this week: most important things learned, theory/big picture. Teaching and pedagogy especially. We went through 10 different workflows in 1 week! Analyzed complex … Continue reading

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GitHub, Pull Requests, and ReadTheDocs – NGS2015

“We’re good enough and deserve github.” Dr. C. Titus Brown shares methods for using readthedocs, which he uses for classes including NGS2015, as well as github and forking pull requests. Sphinx is Python based, readthedocs is web-based method for putting stuff in … Continue reading

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Differential expression and dosage compensation in RNAseq – NGS2015

Dr. Chris Hamm, University of Kansas, side effects of sexual reproduction in Lepidoptera! Explanation of ESA, species status dependent # of self-sustaining populations, Mitchell’s satyr butterfly endangered. Suggests Butterfly People. K-means cluster plots, each vertical bar individual. Michigan different than … Continue reading

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Reproducibility with AWS – NGS2015

Leigh Sheneman, PhD student at MSU in CS. Evolution and learning with digital organisms, applying to real world organisms in the future! http://angus.readthedocs.org/en/2015/week3/AWS-tips.html Start EC2, medium-sized m3.medium is fine. Log in, update and install stuff. We need the packages for the … Continue reading

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GWAS for NGS data – NGS2015

Dr. Tiffany Timbers, postdoc at Simon Fraser University. Became interested in automating and programming from Multiworm tracker, automated image analyses for worm behavioral studies. Today we will use a dataset from 2,007 individuals, 700,000 variants, 20,000 genes potentially contain disruptive … Continue reading

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