- 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.
- Download and install XQuartz https://www.xquartz.org/. This will let you view images from the server.
- Download and install MacDown https://macdown.uranusjr.com/. You'll use this for documenting your work.
- 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!
- 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.
- 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.
- Go to RStudio https://rstudio.com/products/rstudio/download/ and download the FREE version for Mac, then follow the installation prompts.
- Download and install PuTTy https://www.chiark.greenend.org.uk/~sgtatham/putty/. This will let you connect to the server.
- Download and install XMing https://sourceforge.net/projects/xming/. This will let you view images from the server.
- Download and install Joplin https://joplinapp.org/. You'll use this for documenting your work.
- Download and install WinSCP https://winscp.net/eng/index.php. This will let you transfer files to and from your computer and the server.
- 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.
- 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.
- Go to RStudio https://rstudio.com/products/rstudio/download/ and download the FREE version for Windows, then follow the installation prompts.
- tmux cheatsheet https://gist.github.com/MohamedAlaa/2961058
- git book https://git-scm.com/book/en/v2
- R for Data Science https://r4ds.had.co.nz/
Learn basic terminal commands by playing Terminus https://web.mit.edu/mprat/Public/web/Terminus/Web/main.html
- slides
- Practice Exercises
- Command-Line Basic Navigation Practice Exercises, ANSWERS
- slides
- Practice Exercises
- Viewing Files Practice Exercises, ANSWERS
- Navigating the Filesystem Practice Exercises, ANSWERS
- File Wrangling Practice Exercises, ANSWERS
- slides
- Practice Exercises
- Wildcards Practice Exercises, ANSWERS
- Miscellaneous Practice Exercises, ANSWERS
- File Wrangling Part 2 Practice Exercises, ANSWERS
- slides
- Practice Exercises
- I/O Operators Practice Exercises
- slides
- Practice Exercises
- Managing Processes Practice Exercises, ANSWERS
- Running Processes in the Background Practice Exercises, ANSWERS
- References
- tmux cheatsheet https://gist.github.com/MohamedAlaa/2961058
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:
- black
- red
- green
- yellow
- blue
- magenta
- cyan
- white
- default
- slides
- References
- Install git https://git-scm.com/download
- git book https://git-scm.com/book/en/v2
- Adding SSH keys to your GitHub account https://help.github.com/en/github/authenticating-to-github/connecting-to-github-with-ssh
.gitignorehttps://git-scm.com/docs/gitignore- GitHub Desktop https://desktop.github.com/
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.
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.
Went over aligning reads and counting features. All the commands used today are in the slides and the project documentation.
We went over importing, wrangling, and filtering data before testing.
We went over pre-testing visualization, testing, and results visualization.
- differential expression demo code, with updates from today Rmd
We went over gene set enrichment analysis (GSEA) using the fgsea package in R.
- slides
fgseademo code Rmd, updated code from today with how to translate gene names to Entrez IDs Rmd- References
fgseadocumentation, preprint link, pdf- Stephen Turner's
fgseatutorial https://stephenturner.github.io/deseq-to-fgsea/ - GSEA website https://gsea-msigdb.org/gsea/index.jsp
- original GSEA paper link, pdf
- Reactome https://reactome.org
- Packages
We went over RRBS and ran quality control on our sample files.
- slides
- code
- References
- Bismark website http://www.bioinformatics.babraham.ac.uk/projects/bismark/
- Bismark GitHub repository https://github.com/FelixKrueger/Bismark
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.
- slides
- code
- References
- Bismark website http://www.bioinformatics.babraham.ac.uk/projects/bismark/
- Bismark GitHub repository https://github.com/FelixKrueger/Bismark
- data
- code
- Packages
broomvignette https://cran.r-project.org/web/packages/broom/vignettes/broom.htmlpatchworkhttps://patchwork.data-imaginist.com/