Week 2- STAR Alignment

Arnab M -

Hi guys,

It’s Arnab and this is my second weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing. 

Last week my mentor and I designed a complete workflow for the early stages [FastQC→ MultiQC → STAR Alignment] that we’ve been successfully following. As the FastQC stage was completed we utilized another Bioinformatics tool called MultiQC. MultiQC summarizes all of the data collected in our numerous FastQC files and creates visual data graphs/plots (attached in the first image). These tools ensure our data is up to quality and ready to be put through our next stage: STAR Alignment. This is what I started working on in week 2 as STAR Alignment runs and processing can take up to a day, so it is crucial  I did not mess up any code or organization of files for this step (attached in the second image).

STAR Alignment takes the Human Reference Genome (HG38) and compares it to all of our samples to align them together and annotate for differences. The coding to accomplish this was a step up from last week with far more intricacies and complications than last time, but in the end, I followed the STAR Alignment Manuals Coding instructions and successfully created a working code to run STAR which in turn produced BAM files, which I’ll discuss in next week’s blog.

As for more exciting news, the lab has granted me access to their wet lab to view in person some of their other ongoing neurological research on drosophila (fruit flies). I can’t wait to furthermore immerse myself in this translational research and move one step closer to giving children with neurological disabilities a better life.

 

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Comments:

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    Akash Joseph
    This is fascinating, Arnab! I am interested on the coding aspect of your project. We worked on RStudio together earlier in the year. Does this tie into the work we were doing? Super excited to see your results and learn more about BAM files next week!
    February 21, 2024 at 2:55 pm - Reply
    Arnab Misra
    Yeah, so later on in my project once we pass the preliminary steps of FastQC, MultiQC, and STAR Alignment, we move on to the Data Analysis (with more complicated substeps). Every part of Data Analysis is done with a tool from R Studio and that's when our work together will come into play. As for now, our preliminary steps are utilizing the Conda environment, which allows us to download the necessary packages to run our code and once we get deep enough into the project we will use R Studio. Hope this answers your question!
    February 21, 2024 at 4:14 pm - Reply
    camillebennett
    This sounds amazing, Arnab. I'd love to hear more about the neurological research on fruit flies! It is also considerable that you were able to create a working code to run STAR!
    February 22, 2024 at 10:23 am - Reply

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