This past week, I have been doing preliminary assessments with the data that I have gotten back from Xander. For every gene, I used R to examine the kmer abundance distribution, calculate the length (in basepairs) statistics, the percent identity to the gene of interest, and number at 99% identity. I also use R to calculate... Continue Reading →
As I head into week 5, I can't believe the summer program is almost half way over. I just arrived here, but in only about a month I have learned a lot. I am also looking forward to the second half of the program to see what results I will have. This past week I... Continue Reading →
This week I started to impute missing data trait values using a package called multivariate imputation with chained equations (mice). I also used a package called Rphylopars for phylogenetic trees.
This past week I have worked more with the metagenomes. After quality-trimming the files last week, I have started some analysis with the data. Basically, I want to find out the diversity of different arsenic-resistant genes in these metagenomes. To do this I need to find the size of the metagenome by finding the number... Continue Reading →
It's already week 3! Time seems to be going really fast and I can't believe after this week we're going to be almost 1/3 of the way done with the program. This past week, I worked a lot with the HPC by submitting multiple jobs to quality control the DNA sequences and assemble contigs. I've... Continue Reading →
This week I am downloading metagenomes, checking the quality of the data, and quality-filtering the data. To do this, I submit jobs to the HPCC because if I did it all individually on my computer it would take too long. A metagenome is "all the genetic material present in an environment sample, consisting of the... Continue Reading →
My research is on the diversity of arsenic-resistant genes (AsRG) in soil bacteria. Questions that my mentor has been thinking about are: What are AsRG concentrations across soils? How does the diversity of AsRGs change between soils? Can this be mostly predicted or explained by what species make up the community in the soil? Metadata of various... Continue Reading →
This summer will be working under Dr. Ashley Shade with microbiology and molecular genetics. I will be working with my mentor Taylor Dunivin who focuses on bacterial resistance to arsenic, in both forms of arsenate and arsenite. By testing arsenic-resistant genes from various microbial communities in topsoil around the world, it will be possible to quantify a baseline of... Continue Reading →