---
title: "week-07"
output: html_document
date: "2023-05-08"
---

a.  **What is your current grade in the class? How many issues are open in our research repository?**
Grade: 96.57%
Issues: 4 (but I think all have been addressed)

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?**
1. At week 2, it was hard for me to visualize the entire process from the mRNA extraction to analysis. Now, this paper was easier to follow and I could pay more attention to nuances and supplemental information. For example, table 1 seemed overwhelming at first because I didn't quite understand what the analysis methods were, like DGE. Now, I can appreciate the utility of the identification of different analysis software for specific functions. 

2. Without having used visualization software, the "Visualizations" section didn't make much practical sense to me at first. It was hard to wrap my head around what exactly seq data would look like and how it could be manipulated to generate meaningful results. 

Still unclear: I'm still a little unclear as to how libraries are constructed. I don't quite know what goes into that process, though I have heard it can be very time consuming. 

c.  **What is epigenetics and how could it relate to your own research project?**

Epigenetics is the study of mechanisms that change expression of genes without changing the structure of the nucleotides. Some examples include DNA methylation and histone modification that either up-regulates or down-regulates expression of certain genes.  

In snow crabs, epigenetics might play a role in expressing certain genes in response to environmental cues, such as exposure to acidic treatments. 

d.  **Describe what a GFF file is?**

A general feature format (GFF) file is a type of plain text file that is used for describing genomic features. 

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

Describing CG motifs can help us understand gene expression more comprehensively, as they are relatively rare and are often targets of DNA methylation, a common form of epigenetic modification. CG motifs might also illuminate methylation patterns associated with certain diseases. By understanding these patterns, we develop detection methods and treatment.