27 January 2014

expression, Chagas, blast, and RSEM

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Monday notes

  • wrote python script to split large fasta file into many subsets and the submit a batch job to run blastn on each subfile for Chagas project
  • each query takes about 1 minute
  • 5,000 queries would take about 3.5 days
  • meet with Grace
  • painted ants into two groups (blue, red) for thermal treatments


Checked input files - does not appear that A22 and Ar were accidentally duplicated in the trimming step.

Installed RSEM from github

Added both RSEM and Sailfish to path \etc\bash.bashrc so they would be globally available.


{r, echo=FALSE, results='hide'} library(knitcitations)

Hargreaves, A.L., Samis, Karen E. & Eckert, C.G. (2014). Are Species’ Range Limits Simply Niche Limits Writ Large? A Review of Transplant Experiments beyond the Range. The American Naturalist, 183, 157–173.

  • very nice meta-analysis of range limit research
  • includes my 2012 Oecologia paper!

Kiełbasa, S.M., Wan, R., Sato, K., Horton, P. & Frith, M.C. (2011). Adaptive seeds tame genomic sequence comparison. Genome Research, 21, 487–493.

  • faster alignment than BLAST
  • uses adaptive, rather than fixed, seeds
  • Program available here

Bocedi, G., Palmer, S.C.F., Pe’er, G., Heikkinen, R.K., Matsinos, Y.G., Watts, K. & Travis, J.M.J. (2014). RangeShifter: a platform for modelling spatial eco-evolutionary dynamics and species’ responses to environmental changes. Methods in Ecology and Evolution, n/a–n/a. Retrieved January 27, 2014,

RangeShifter fills a major gap in the field of eco-evolutionary research byproviding a user-friendly platform that will make individual-based simulation of species’ dynamics on realistic landscapes much more accessible to stakeholders.


Data visualization

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