### Week 02 Question Set

a)  **What do you feel was the most impressive thing you did in class last week was?**
I feel conflicted with this question as I don't feel as i did impressive work because i required a lot of help as i am pretty new to coding. Something I was glad that I could do is that there was some troubleshooting that i wanted help on but then I looked over the code more closely and realized something was just missing a space or ~. I felt like i was learning to pay more attention on that. 

b)  **What is your weekly goal for making progress on your project? What is the next step?**
I am still trying to figure out what exactly my project is and i have a better idea of maybe doing a pangenome of SAR11 and seeing all the transport and catabolic genes related to metabolite utilization. It could tell me all the common gene clusters of all known SAR11 genomes and see how diverse is their diet.However, I am not completely sure how I can start this? I have found some workflow in the internet in how I can approach it but ideally I would like to see how to incorporate it into my project here. 
Maybe a goal would be starting the connection of what tools to use to begin an outline for my project. 

Also this is the website for some thoughts i had to do my project?

https://merenlab.org/2016/11/08/pangenomics-v2/


c)  **There were two readings this week not from the textbook, meant for two different audiences. Which reading did you get the most out of and why? Do you have any questions regarding the Journal of Shellfish Research paper?**
I got the most from the Journal of Shellfish research paper. I am not an expert in RNAseq and I am not advanced enough to fully perform all the coding shown in the Fitting Multifactorial Models of Differential Expression. I did feel like I started seeing certain R functions I am learning and saw new onws so that was increasing my exposure. Now from the Journal of Shellfish, I learned a lot of the methods and how all together what the experiments that are performed and why are they performed to their analyzes. I think it was nice to have latter review it all because now I understand a bit more of what RNAseq does and how bioinformatics comes into play to understand its output. 

I do not have any further questions. It was a great read.

d)  **What is your favorite thing about markdown and why?**

I havent use Markdown before but I am finding that the ability of including bash, python and R code within one place has been very interesting and makes me think of the other possibilities or the power markdown might have. So I would say that interdisciplinary condition is my favorite thing. 

e) **What is the difference between 'curl' and 'wget'? When would you use one over the  other?**

From my understanding 'curl' will show the output while 'wget' will download it into the file. You would want to use one over the other depending on your purpose. If you just want the output then using 'curl' is fine but if you would want the output embedded somewhere into the file then 'wget' is better because it is doing more than 'curl' is.