Scientific-experiment-in-progress

It is not often that I am allowed to work on wet-bench experiments, as I am a programmer by trade. On Friday I had an idea to test some of our sequencing samples, and today we are going to try to put the idea into practice and see what we can come up with. It is always exciting to experiment outside of my traditional role as a bioinformatics analyst, and in all honesty it is extremely helpful to see how the other half lives and works, because the more I understand how experiments are preformed and all of their caveats, the better I can understand the output data and how best to utilize it.

Today’s work can be summed up in this nice graphical image via Wikipedia:

787px-CoT_analysisBasically, the idea is to see if we can detect and evaluate how much unique DNA is present in a sequencing library (library is what we call something that is ready for sequencing, as in a “library” of DNA). The idea is that for bad samples, we have many copies of the same fifty-base string (think ACGTACGT). For good samples, we have many, many different combinations of the ACGTs, meaning it is more “complex.” The more complex a sample, the better off the results are after sequencing. My hope is that we might be able to save money by not sequencing not very complex samples, as it results in junk output anyway. Kinda a simple breakdown of the idea, but who knows! Maybe it’ll actually  work.

Anyways, hope it goes well!