Cheat Sheets

Cheat Sheets

Monday

• Welcome
• Logging In and transferring files
• Intro to command-line (talk)
• Intro to command-line walk-through
• Intro to command-line files
• Advanced command-line
• Running jobs on the Cluster and using modules

Tuesday

• Intro to Sequencing, Lutz Froenicke (talk)
• Files and Filetypes for RNA-Seq (talk)
• Project Setup hands-on
• Workshop dataset (talk)
• Lunch and Learn - Kapa Biosystems
• Preprocessing Data hands-on
• Experimental Design and Cost Estimation (talk)

Wednesday

• More Files and Filetypes for RNA-Seq (talk)
• Aligners
• Aligners hands-on
• Lunch and Learn - Qiagen
• Generating Summarized Counts

Thursday

• Intro to R
• Lunch and Learn - Lexogen
• DE Analysis: counts to lists of DE genes
  • The R Markdown file

Friday

• Gene Ontology and KEGG Pathway Enrichment Analyses
  • The R Markdown file
• Generating figures
  • The R Markdown file
  • I5_v_C_time6.txt
  • I5_v_C_time6_KEGG.txt
  • metafile
  • all_counts.txt
  • all files for plots
• Closing thoughts

Other Talks

What is Bioinformatics Transcript assembly Single Cell RNAseq Spacial Transcriptomics