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A Summer of Internship: Week 2-3 at Adebali Labs

A Summer of Internship: Week 2-3 at Adebali Labs

Week 2: A Deep Dive into .bed Files and Normalization Techniques 📊

Hey all! Week 2 at Adebali Labs was a blend of technicalities and hands-on experiences. Let's get into the DNA of the week, shall we?

.bed Files: The Genomic Blueprint 🧬

This week's most significant highlight was undoubtedly .bed files. Picture this: a structured list giving you the lowdown on every tiny detail of a gene. Yep, that’s a .bed file for ya.

Sample .bed file

Here’s a quick breakdown for the uninitiated:

  • Chrom: Which chromosome we're talking about.
  • Start & End: Think of these as the ‘start’ and ‘end’ lines of code but for genes.
  • Gene_id: The unique ID every gene flaunts.
  • Gene_name: The more formal name for the gene.
  • Strand: Identifies the specific DNA strand.
  • Counts: The frequency counter, marking repair action on that gene segment.
Sample of our data

Normalization: Keeping it Consistent 🔄

Then, we delved into the normalization waters, focusing mainly on RPKM and its log-transformed twin, log_rpkm. Normalization is essential to keep our data consistent and reliable.

To sum up Week 2, it was a blend of understanding genomic blueprints and ensuring data reliability. I got to see how the raw genomic data was structured and prepped, setting me up for the more analytical adventures in Week 3.

Week 3: Drawing Connections with Correlation 🤝

Hey peeps, Week 3 was all about drawing the dots and seeing the patterns, aka correlation. Let's decode the week!

Unraveling the Threads of Data 🧶

Correlation is essentially understanding how one set of data behaves in relation to another. For our research, this was essential to see the connections between different genomic repair metrics.

Through this analysis, I identified specific genomic sequences that held potential in predicting repair metrics, setting the stage for the more in-depth statistical modeling next week.

And that's a wrap on Week 3! From .bed files to intense correlation analysis, I'm loving this blend of biology and data analytics. Can't wait for the next set of adventures!

Till the next post – keep exploring✨🔍