Week 1- FastQC

Arnab M -

Hi guys, 

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

Today was my very first day in person at Dr. Kruer’s Lab at the Arizona Biomedical Campus in Downtown Phoenix. I got the incredible opportunity to meet one of my research mentors Dr. Bisarad, a postdoc, for the very first time in person and start on our intricate and fascinating research journey. A week ago, my bioinformatics research team worked with TGen (The Translational Genomics Institute) to design our workflow plan (that’ll keep updated on as we progress through the project). The basic oversimplified steps our lab and TGen have designed in our workflow are as follows:

FAST QC → STAR Alignment → DESeq 2→ Data Analysis 

Today, we tackled FAST QC. This is a process in Bioinformatics research where we take raw data, previously collected by the lab from patients, and test their quality, hence the QC (Quality Control). This is when we delved into the coding world of Bioinformatics where I learned specific commands and syntax in shell script (coding language). This coding is vital to perform and analyze the patient data as a simple line of code from hundreds of samples can be analyzed with a simple push of the enter key. In my first attached picture, you can see the code we ran on a sample, to test it out, and the second picture shows the FASTQC Report that has metrics to measure the quality of data we have. Typically, every box should be green checked, however, in a few samples the “Overrepresented Sequences” and “Sequence Duplication” posed some errors. This is when more tools of Bioinformatics would come into play, so you can ensure your data is of the highest quality, however, this is a task that will be accomplished in my next session at the lab. For now, we took all our data files and ran them through my simple yet elegant piece of code, as shown in Picture 3, which will take ~3 hours to fully process as our first reads through FastQC, and later on we will use other tools to make sure all those boxes are ticked green in the FastQC report.

It was a privilege to meet such accomplished and motivated researchers who pour their heart and soul into fighting CP, and I can’t wait to see where this research project takes me next week!

Picture 1
Picture 2
Picture 3

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    It's cool to hear how the raw data is analyzed with the FAST QC to ensure quality. I'll be following along as you continue your research with Dr. Kruer's lab and TGen, and I look forward to hearing about your progress as you complete the other steps of the lab!

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