NGS_Onboarding

This respository is designed to help new lab members with on-boarding tasks for Biowulf and NGS analysis in the Batista Lab.

Getting Started on Biowulf

1. Request a Biowulf account here
2. Once you have an account, request that @FitzsimmonsCM (our Biowulf admin) add you to the appropriate group directories on Biowulf.
3. Follow our lab instructions to update your default permissions, and ensure that you can navigate to the shared directories.
4. Ask @FitzsimmonsCM or @BatistaLab add you to the lab GitHub.
5. Get started!

A Few of Our Favorite Things

We recognize that everyone comes to our lab with different levels of coding experience. To help everyone learn, we've compiled a list of our favorite resources. This list is not meant to be exhaustive, but let us know if you have a favorite resource we can add or if one of the links is broken.

Programming-specific text editors

Using a programming-specific text editor makes it easy to write code accurately without formatting issues. Here are a few text editors that members of our lab use. Try a few and select the one that you like. Importantly--DON'T USE WORD OR GOOGLE DOCS TO WRITE CODE

• Komodo Edit
• Notepad++
• BBEdit
• Sublime Text
• Visual Studio Code

Resources for Biowulf and high-performance computing

1. Biowulf user guide
2. Biowulf online learning guide
   • Biowulf Basics (how to login, when should I use the cluster, etc)
   • How to access applications on Biowulf
   • How to submit a batch job
   • How to submit a job swarm
   • Information about job resources (walltimes, partitions, job scheduling, etc)
   • Information about job dependencies
   • Connecting a Jupyter Notebook to Biowulf
3. Globus file transfer

Resources for GitHub and Branching

1. Installing GitHub Desktop
2. GitHub skills lab has many courses for beginners and advanced programers.
   • introduction-to-github
   • communicate-using-markdown
   • review-pull-requests
   • reusable-workflows
3. Learning Git Branching visual interactive tool

Resources for R and Rstudio

1. Downloading R and Rstudio
2. R 4 Data Science textbook
3. Base R cheatsheet
4. dplyr cheatsheet
5. ggplot cheatsheet
6. TidyTuesday by the R4DS community

Resources for Python

1. Python Tutorial
2. Project Euler free mathematical / computer programming problems
3. Learn Python the Hard Way

Resources for bash

1. Shell scripting basic commands
2. Command line Crash Course
3. A basic unix tutorial
4. Unix tutorial for beginners
5. BashVenture a text-based game

Resources for bioinformatics

1. bedtools sandbox
2. Analyzing RNA-seq data with DEseq2
3. UCSD Bioinformatic Club Introduction to Bioinformatics
4. Project Rosalind learn python and bioinformatics through free problems