Coriell Bioinformatics Server Lessons

Getting Started

Mac

  1. You’ll connect to the server through terminal, so you don’t need to install any software. I suggest pinning terminal to the dock though.
  2. Download and install XQuartz https://www.xquartz.org/. This will let you view images from the server.
  3. Download and install MacDown https://macdown.uranusjr.com/. You’ll use this for documenting your work.
  4. Download and install Macfusion. Follow the directions here. This will let you transfer files to and from your computer and the server. This is the hardest thing to install, so if it doesn’t work come ask for help!
  5. You should already have the Cisco AnyConnect VPN installed on your computer, but if you don’t, follow the instructions here. This will allow you to connect to the server from outside of Coriell.
  6. Install R. Go to R Cloud https://cloud.r-project.org/ and click on “Download R for (Mac) OS X” and follow the instructions and your computer prompts.
  7. Go to RStudio https://rstudio.com/products/rstudio/download/ and download the FREE version for Mac, then follow the installation prompts.

PC

  1. Download and install PuTTy https://www.chiark.greenend.org.uk/~sgtatham/putty/. This will let you connect to the server.
  2. Download and install XMing https://sourceforge.net/projects/xming/. This will let you view images from the server.
  3. Download and install Joplin https://joplinapp.org/. You’ll use this for documenting your work.
  4. Download and install WinSCP https://winscp.net/eng/index.php. This will let you transfer files to and from your computer and the server.
  5. You should already have the Cisco AnyConnect VPN installed on your computer, but if you don’t, follow the instructions here. This will allow you to connect to the server from outside of Coriell.
  6. Install R. Go to R Cloud https://cloud.r-project.org/ and click on “Download R for Windows” and follow the instructions and your computer prompts.
  7. Go to RStudio https://rstudio.com/products/rstudio/download/ and download the FREE version for Windows, then follow the installation prompts.

Resources

Server Basics

Week 1 - Terminus - 2019-10-22

Learn basic terminal commands by playing Terminus https://web.mit.edu/mprat/Public/web/Terminus/Web/main.html

Week 2 - How to Use the Server - 2019-10-29

Week 3 - How to Use the Server, cont. - 2019-11-05

Week 4 - How to Use the Server, cont. - 2019-11-12

Week 5 - How to Use the Server, cont. - 2019-11-19

Week 6 - How to Use the Server, cont. - 2019-12-03

Change the color of the bottom bar in tmux

Thanks to Himani for asking and this Stack Exchange post https://unix.stackexchange.com/questions/60968/tmux-bottom-bar-color-change/60969, here’s how you change the color of the bottom bar in tmux.

In tmux, hit Ctrl-B, then type :set status-style "bg=magenta". Replace magenta with another color from the list for other colors.

Possible colors:

Git

RNA-seq

Process RNA-seq Week1 - 2020-01-07

Briefly went over how Illumina sequencing works and the types and structure of FastQ files. Also set up our project folders including GitHub repositories. The project documentation contains all of the commands we used today, except for where to find your SSH key, which is in the slides.

Process RNA-seq Week2 - 2020-01-14

Went over the FastQC program and it’s output report and why we trim reads. Ran FastQC and trimming. Will go over results of trimming next week. All commands used today are in both the slides and the project documentation.

Process RNA-seq Week3 - 2020-01-21

Went over aligning reads and counting features. All the commands used today are in the slides and the project documentation.

Differential Expression Week 1 - 2020-01-28

We went over importing, wrangling, and filtering data before testing.

Differential Expression Week 2 - 2020-02-04

We went over pre-testing visualization, testing, and results visualization.

Differential Expression Week 3 - 2020-02-11

We went over gene set enrichment analysis (GSEA) using the fgsea package in R.

Reduced Representation Bisulfite Sequencing (RRBS)

Process RRBS Week 1 - 2020-02-21

We went over RRBS and ran quality control on our sample files.

Process RRBS Week 2 - 2020-03-03

We finished running through the RRBS processing pipeline. Note the change in the final methylation count / methylation extraction command to delete the unnecessary read level methylation context files.

Analyze RRBS Week 1 - 2020-03-10