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title: "Week 06 Questions"

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a)  **What is your current grade in the class? How many issues are open in our research repository?**

My current grade is 97%. In the private assistance repo there are 23 issues open and in the public assistance repo there are 14 issues open.

b)  **Re-reading this week's reading, what are 2 things that resonate with you now that made little practical sense in week 2. What is one aspect that you still wonder about or is unclear?**
Two things that better resonate with me now are: 1) The need for proper data management mechanisms for the large amount of data produced even from a handful of RNAseq files. 2) Understanding how to manipulate files in the command line. Something that may be useful to further delve into, is integratino of quality control and assessment into the workflow from running something like MultiQC.

c)  **What is epigenetics and how could it relate to your own research project?**
The epigenetic effects that occur due to exposure to carcinogens in primary cell cultures of model organisms has been widely studied. In that vain, I could potentially investgate the changes in DNA methylation in primary cell cultures of *Botryllus schlosseri* exposed to carcinogens like nickle chloride.

d)  **Describe what a GFF file is?**
A gff file is a general feature format tab-seperated file that generally contains 9 columns with each row containing information regarding a single gene. It is how annotations for genomes are stored and are necessary in a DEG analysis.

e)  **What are two ways describing CG motifs could have value?**

Given CpG motifs play in important role in DNA methylation, describing them may be useful in describing potential epigenetic changes. In this way, CpG motifs could potentially also be useful in identifying onset of disease such as oncogenesis in cells.