For this week’slab meeting, Trung presented this paper to the lab. Jin, Y. H., Clark, A. B., Slebos, R. J., Al-Refai, H., Taylor, J. A., Kunkel, T. A., … & Gordenin, D. A. (2003). Cadmium is a mutagen that acts by inhibiting mismatch repair. Nature genetics, 34(3), 326-329.
Month: October 2017
Lab meeting 10/18/2017
Papers that were discussed in this week’s lab meeting. Kenny: Ebert, D., Joachim Carius, H., Little, T., & Decaestecker, E. (2004). The Evolution of Virulence When Parasites Cause Host Castration and Gigantism. The American Naturalist, 164(S5), S19-S32. doi:10.1086/424606 Swatantra: Akbar S, Du J, Jia Y, Tian X (2017) The importance of calcium in improving resistance of Daphnia to Microcystis. PLOS ONE 12(4): e0175881.https://doi.org/10.1371/journal.pone.0175881 Trung: Bodar, C. W. M., Van Leeuwen,…
Lab meeting 10/11/2017
Papers we discussed were: Marelize: Asselman, Jana & I. M. De Coninck, Dieter & Beert, Eline & Janssen, Colin & Orsini, Luisa & Pfrender, Michael & Decaestecker, Ellen & A. C. De Schamphelaere, Karel. (2016). Bisulfite Sequencing with Daphnia Highlights a Role for Epigenetics in Regulating Stress Response to Microcystis through Preferential Differential Methylation of Serine and Threonine Amino Acids.…
STAR RNA-seq mapping on Stampede2
After multiple round of experimenting, I found out an alternative way to run RNA-seq mapping with STAR on Stampede2 would be to use a whole node (16 cores) at the same time. The DDR RAM for a node on Stampede2 is 96 Gb,which may not be enough for handling multiple independent mapping jobs. We can use multiple threads for STAR…
Use Launcher to bundle multiple serial jobs on Stampede2
As I was exploring Stampede2 at TACC for more RNA-seq data analysis, I needed to map the RNA seq reads for 68 samples to the Daphnia genome. Because on Stampede2, even a single serial job with 1 cpu would take the entire resources of the entire node of 16 cpus. I decided to use the tool launcher that built in…
Lab meeting 10/4/2017
We discussed these papers in lab meeting 10/4/2017. Swatantra: Pastenes, L., Valdivieso, C., Di Genova, A., Travisany, D., Hart, A., Montecino, M., Orellana, A., Gonzalez, M., Gutiérrez, R.A., Allende, M.L. and Maass, A., 2017. Global gene expression analysis provides insight into local adaptation to geothermal streams in tadpoles of the Andean toad Rhinella spinulosa. Scientific Reports, 7. Kenny: Urabe, J., & Sterner,…