Research Topics

• Study associations between genetic variants and complex diseases
  • Genome-wide Association Studies. Lecture slides are available from YangLabWebsite.
  • Transcriptome-wide Association Studies; Proteome-wide Association Studies; Integrate multi-omics data
• Study RNAseq data: Differential Gene Expression Analysis
• Develop disease risk prediction model
• Clinic WES analysis
• Method, tool, pipeline development, application studies

Real Data Formats

• Genetic data: VCF format (text), Plink BED/BIM/FAM format, BIMBAM format (text)
• RNA Sequencing data: fastq (text), BAM (binary version of SAM), RPKM/TPM text
• Phenotype data: PED (text), tsv, csv
• Annotation data: BED (text)
• Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS) data: fastq (text), BAM (binary), VCF

Programming languages and tools

• R, Python, C++
• Human genetics cloud computing (HGCC) and RHPC server
  • Linux commands; Bash scripts
  • Introduction to HGCC and Bash is available from YangLabWebsite
• Linux tools for data handling
  • AWK, grep, gzip, zcat, sort, the pipe "|"
  • BCFtools, BEDtools, Samtools; TABIX, Plink
• AWS

Working Tips

• Mont cloud directories to local computer and use local code/text editor such as VScode and Sublime to edit scripts
• Write bash scripts for your jobs
• Use Markdown (e.g., Rmarkdown, MacDown) to write Project Summary
• Be motivated and organized

Data/Code Sharing

• Emory Onedrive
• HGCC/RHPC
• Github

Suggestions

• Allocate blocks of working time (>2 hours)
• Update your to-do list regularly
• Document your work progress
  • Organize your results for discussion
  • Write a paper outline for your project
  • Put your work on Github, one directory per project

Suggestions

• Keep your HGCC/RHPC home directory organized and avoid saving duplicate copies of the data
• Attend selective journal clubs, seminars, workshops
• Attend group, department, school activities to interact with collegues, staff, professors, etc.
• Ask around for help

Lab Meeting Format

• All members take in turn to lead the discussion

  • Present one’s research progress
  • Discuss a paper as a journal club

• Group discussion and hangouts

• In person for Fall 2022 (Whitehead 3rd Floor) with zoom options

Tips 2022

• ResearchRabbit : Organize reference papers and find connected papers
• Text Compare : Compare two text files to show differences, e.g., Sublime Package Compare Side-By-Side
• Note App : Notion, OneNote, Evernote
• Reference Manager Software : Zotero, Endnote
• Markdown tools : MacDown for writing simple markdown file; MMarp for VS Code for writing slides.

Tips 2022

• Use Docker for software development : Avoid the hassel of setting up local environment
• Pipe data in R scripts : %>% or |> with fast key cmd + shift + m
• Write comments and use informative variable names and function names during programming
• Useful R libraries for data science: tidyverse, data.table, caret
• See YangLabTeaching webpage for more resources about recent course slides, scientific writing, and scientific presentations.
• Be Organized

Lab Activities

Tingyang is our Lab Activity Manager!

• Lunch hangouts
• Outdoor hangouts
• Birthday and holiday celebrates

Birthdays

• Jingjing 1/4
• Randy 3/1
• Shizhen 4/5
• Tingyang 7/22
• Qile 8/5
• Rebecca 10/28
• Shuyi ?

Exiting the lab

• Clean and organize your HGCC home directory
  • Delete redundant content
  • Write README.md file for your directories to describe file contents
• Delete real data from your local computer
• Write a summary project report including directory information of your data, results, and scripts