New Member Reading and Exercises

Topics to familiarize yourself with

• Common bioinformatics file formats
  • BED, GFF3/GTF, FASTA, FASTQ, SAM/BAM
  • Look at "Read More" links in ScriptManager docs: https://pughlab.mbg.cornell.edu/scriptmanager-docs/docs/Guides/Getting-Started/file-formats
• Common genomics assays within our lab/field:
  • ChIP-exo vs ChIP-seq
  • ATAC-seq
  • RNA-seq
  • PRO-cap/PRO-seq/CoPRO (see John Lis’s lab for papers about these last few, he is our neighbor on this floor)
  • Enseqlopedia gives high-level summaries of what these assays measure: https://enseqlopedia.com/
• Learn the basics of command line

Recommended Reading

• Rossi et al 2021 - Yeast Epigenome (YEP) paper
  • https://github.com/CEGRcode/2021-Rossi_Nature/tree/master
• Rossi et al 2018 - Simplified ChIP-exo paper
  • https://www.nature.com/articles/s41467-018-05265-7
• Arslan et al 2023 - Avidite sequencing (AVITI) paper
  • https://www.nature.com/articles/s41587-023-01750-7
  • Animation of Avidite sequencing from Element Biosciences: https://www.youtube.com/watch?v=b_cC5wi2OYg
• Noble et al 2009 - Organizing your bioinformatics projects
  • https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424

Exercises to work through

1. ChIP-exo tutorial
   • An introduction to using ScriptManager's GUI and some core tools within the suite
2. Reproduce one of the YEP paper (Rossi 2021) Fig 3 subpanels in plotter
   • Use data downloads from www.yeastepigenome.org
   • An introduction to using plotter
3. "Linux for Biologists" workshop
   • An introduction to basic shell scripting
4. Learning Git
   • Using Github Desktop video tutorial
   • Understanding how branching and merging in git interactive exercise
   • It's also important you learn to write good commit messages and titles

Optional bonus resources

1. RSE Training
   • We recommend topics like Vim, Git, and the INTERSECT materials
2. PSU Biostars Bootcamp #day2
   • Understanding Shell scripts, Markdown, Git and start using ACI clusters.
3. Beginner Web Development tutorials MDN Web Docs
   • Web technologies at a glance.
   • HTML
   • CSS
   • Javascript
4. Understanding React
   • Why did they build React ?
   • Official React docs
5. Creating REST API with Node.js
   • video tutorial
6. Creating React Applications
   • video tutorial
7. CULearn has a broad variety of courses if you use your Cornell NetID login