Welcome to the Miller Lab RADSeq/RAPTURE pipeline. This website is a work-in-progress, but provides much of the protocols, pipeline, and code used in population genomic analyses. A summary of what is on this site is as follows:

Background tab has has info on coding using bash, how to connect to the cluster and to sftp as well as some additional R coding resources.

Downloading Data provides info on how to get your data, split by plate, split by barcode, and add metadata.

Alignment describes the main ways data will be aligned, (either de novo or reference

Filtering shows how to filter data for quality and number of reads. The subsample script will select all bams with reads above a given threshold, and then randomly subsample to exactly that threshold of reads (e.g., so all samples have exactly 100k reads).

PopGen Analysis shows a number of different analyses that can be done. Work in progress.

Pipelines provides a few complete pipelines (as-is) that are used by different researchers and datasets as examples.

Post Analysis describes how to upload data to NCBI for archival purposes.

SF Eel - Elder Ck

SF Eel - Elder Ck

Software Setup Instructions

R and RStudio

R and RStudio are separate downloads and installations. R is the underlying statistical computing environment. RStudio is a graphical integrated development environment (IDE) that makes using R much easier and more interactive. You need to install R before you install RStudio.

Windows

If you already have R and RStudio installed
  • Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.
  • To check which version of R you are using, start RStudio and the first thing that appears in the console indicates the version of R you are running. Alternatively, you can type sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it. You can check here for more information on how to remove old versions from your system if you wish to do so.
If you don’t have R and RStudio installed
  • Download R from the CRAN website.
  • Run the .exe file that was just downloaded
  • Go to the RStudio download page
  • Under Installers select RStudio x.yy.zzz - Windows XP/Vista/7/8 (where x, y, and z represent version numbers)
  • Double click the file to install it
  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.

macOS

If you already have R and RStudio installed
  • Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.
  • To check the version of R you are using, start RStudio and the first thing that appears on the terminal indicates the version of R you are running. Alternatively, you can type sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it.
If you don’t have R and RStudio installed
  • Download R from the CRAN website.
  • Select the .pkg file for the latest R version
  • Double click on the downloaded file to install R
  • It is also a good idea to install XQuartz (needed by some packages)
  • Go to the RStudio download page
  • Under Installers select RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit) (where x, y, and z represent version numbers)
  • Double click the file to install RStudio
  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.

Linux

  • Follow the instructions for your distribution from CRAN, they provide information to get the most recent version of R for common distributions. For most distributions, you could use your package manager (e.g., for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora sudo yum install R), but we don’t recommend this approach as the versions provided by this are usually out of date. In any case, make sure you have at least R 3.3.1.
  • Go to the RStudio download page
  • Under Installers select the version that matches your distribution, and install it with your preferred method (e.g., with Debian/Ubuntu sudo dpkg -i rstudio-x.yy.zzz-amd64.deb at the terminal).
  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.

Spreadsheet program

To interact with spreadsheets, we can use LibreOffice, Microsoft Excel, Gnumeric, OpenOffice.org, or other programs. Commands may differ a bit between programs, but general ideas for thinking about spreadsheets are the same.

For this lesson, if you don’t have a spreadsheet program already, you can use LibreOffice. It’s a free, open source spreadsheet program.

Windows

  • Download the Installer
    • Install LibreOffice by going to the installation page. The version for Windows should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  • Install LibreOffice
  • Once the installer is downloaded, double click on it and LibreOffice should install.

Mac OS X

  • Download the Installer
    • Install LibreOffice by going to the installation page. The version for Mac should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  • Install LibreOffice
  • Once the installer is downloaded, double click on it and LibreOffice should install.

Linux

  • Download the Installer
    • Install LibreOffice by going to the installation page. The version for Linux should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  • Install LibreOffice
  • Once the installer is downloaded, double click on it and LibreOffice should install.


These setup instructions are adapted from those written for Data Carpentry: R for Data Analysis and Visualization of Ecological Data and Data Carpentry: Data Organization in Spreadsheets.