MY FIRST TIME USING CLC

    It's definitely been a while since I've updated my blog (I've been very busy over the past two weeks as the semesters about to start reaching its closing point). But, about a week-and-a-half ago, I started working a little bit with CLC (a genomics workbench used to analyze the microbial species present in our sourdough starters).

MY EXPERIENCE

    The process of working through the protocols in CLC was actually a bit easier than I expected. I noticed that the direction said that it would take a while and it might be pretty challenging, so a part of me was definitely worried that it would be too difficult for me to figure out. However, by making sure that I was following the directions (and by doing exactly what was happening in the screenshots), everything went smoother than I expected it would.
    While the process was definitely easier than I expected, it took just about the amount of time I thought it would. I worked on it for a couple hours last Wednesday or Thursday and finished it up the next day (either Thursday or Friday).
    I feel like the steps were laid out in a very thorough and organized fashion, meaning everything made sense for the most part. The part that I had the most difficulty with was figuring out which elements to select from the "select sequencing reads"; at first, I selected EVERY SINGLE ELEMENT. This led to a workbench that didn't have the ability to properly analyze the data and me, sitting there in frustration for about thirty minutes trying to figure out went wrong. 
    After I looked at the screenshots and found that I was only supposed to select the paired data, everything became a lot less stressful and it felt like it went smooth sailing from there (I started also looking to the pictures for guidance, instead of just the text).

USING GRAPHS TO ORGANIZE DATA

Sunburst view of fungal species for all samples.



Sunburst view of fungal species for sample ten.

    Above are the sunburst graphs I composed for the fungal species in all the samples and the one just for sample ten. From the graphs, we find that Eurotiomycetes are the primary fungi species present in our starters. 
    One interesting take away I found from these two graphs is that sample ten contained more Mucoromycetes and Agaricomytes than the other samples. I wonder, if other samples that contain similar fruits have a VERY SIMILAR microbial composition for fungi?

QUESTIONS FROM THIS DATA

The questions I have from this week's data are the same as those I had last week:

1.) Do "thicker/starters with medium thickness" banana starters have different microbial compositions than "thinner" banana starters? Basically, I want to see if the thickness of starters affects the types of microbes or ratio of microbes present in our different starters. For this question, I feel as though you'd have to sequence each of the banana starters on their own and ensure to track their thickness when collecting the data.

2.) Do starters with fruits classified as "bitter", have rising rates that differ from fruits that are classified as "sweet"? With this question, I want to explore if fruits that have differing tastes have microbial communities with differing compositions.

3.) Do fruits with similar rising rates have microbial compositions that are similar/the same to other fruits with a similar rising rate? Finally, I wanted to explore if fruits with differing rising rates had varying microbial compositions.

TO BE CONTINUED...

    Overall, I feel as though the CLC workbench helps us better visualize and understand our data. With this being said, it is a difficult program to navigate if you're a beginner (although, it was slightly easier than I expected) and took a decent amount of time. However, CLC may be the key to help me answer some of my questions, such as "do fruits with similar rising rates have microbial compositions that are similar/the same to other fruits with a similar rising rate?"



Author's Note: I'm Calyssa Stevenson and I'm currently a second-year student at North Carolina State University, studying Horticultural Science. This blog is meant to serve as a way to document my sourdough journey and the microbial compositions of my sourdough for my Genetics Lab. Thank you so much for reading! :)



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