Getting your project started¶

Project organization is one of the most important parts of a sequencing project, but is often overlooked in the excitment to get a first look at new data. While it’s best to get yourself organized before you begin analysis, it’s never too late to start.

You should approach your sequencing project in a very similar way to how you do a biological experiment, and ideally, begins with experimental design. We’re going to assume that you’ve already designed a beautiful sequencing experiment to address your biological question, collected appropriate samples, and that you have enough statistical power. For all of those steps, collecting specimens, extracting DNA, prepping your samples, you’ve likely kept a lab notebook that details how and why you did each step, but documentation doesn’t stop at the sequencer!

Every computational analysis you do is going to spawn many files, and inevitability, you’ll want to run some of those analysis again. Genomics projects can quickly accumulates hundreds of files across tens of folders. Do you remember what PCR conditions you used to create your sequencing library? Probably not. Similarly, you probably won’t remember whether your best alignment results were in Analysis1, AnalysisRedone, or AnalysisRedone2; or which quality cutoff you used.

Luckily, recording your computational experiments is even easier than recording lab data. Copy/Paste will become your best friend, sensible file names will make your analysis traversable by you and your collaborators, and writing the methods section for your next paper will be a breeze. Let’s look at the best practices for documenting your genomics project.

Your future self will thank you.

References¶

[A Quick Guide to Organizing Computational Biology Projects] (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424)

Download and Test

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.