Bioinformatics and Functional Genomics 3rd Edition

Chapter 8: DNA: The Eukaryotic Chromosome

In Chapter 8 we discuss the eukaryotic chromosome. Topics include (1) General features of eukaryotic chromosomes, (2) Repetitive DNA content, (3) Gene content, (4) Regulatory regions, (5) Comparison of eukaryotic DNA, (6) Variation in chromosomal DNA, and (7) Techniques to measure chromosomal change.

For those who are unfamiliar with the R programming language, I encourage you to try it. On your PC or Mac, download and install the freely available R program (from http://r-project.org), then install RStudio (from http://www.rstudio.com). The web documents for this chapter (and others) include "R markdown" (.Rmd) files. Here are several R markdowns (and the corresponding HTML file that's created by entering"Knit HTML" in RStudio):

Solution to computer lab problem 8.3 Link to chapter8problem3.Rmd or chapter8problem3.html
Solution to computer lab problem 8.4 Link to chapter8problem4.Rmd or chapter8problem4.html
Solution to computer lab problem 8.11 Link to chapter8problem11.Rmd

Download one to your desktop or other directory; open RStudio, and set the working directory to your desktop; then open the R markdown file. You'll see that RStudio includes a panel (at top left) showing the commands, and as you navigate to a line and click "run" that command is implemented. You can follow the scripts all the way through an R markdown file to answer a broad variety of questions such as "what genes are in a particular region?" or "what repetitive elements are shared between two organisms?" or "given a list of accession numbers of some sort, what are the official gene symbols, what is the GC content of those genes, and which of them encode transmembrane domains? Once you know how to use a few R packages you can ask and answer thousands of questions.

There are fantastic (and free) resources to get a gentle introduction to R. Try swirl at http://swirlstats.com/, Code Academy at https://www.codecademy.com/, Software Carpentry at https://software-carpentry.org/, or other places listed in Chapter 1 of this book. And be sure to visit Biostars (https://www.biostars.org/) to see other peoples' questions and answers!