August 2018 Microbial Community Analysis Workshop

August 6-10, 2018

Cheat Sheets

Cheat Sheets

Intro Command Line Material

• Intro to command line (short talk)
• Intro to command line (materials)

Lectures

• What is Bioinformatics? (talk)
• Intro to Microbial Sequencing/Experimental Design (talk)

dataset metadata

• sample submission
• barcode table
• primer table
• sample sheet

dbcAmplicons

• Installing Software (materials)
• dbcAmplicons: Amplicons (talk)
• dbcAmplicons: Bioinformatics (talk)
• dbcAmplicons: Data processing, 16S V1-V3 (materials)
• dbcAmplicons: Data processing, other amplicons (materials)

Intro R Material

• Intro to R
  • raw_counts.csv
  • raw_counts.txt
• Data in R
  • prepare
  • Data in R
  • Data in R Rmd file
  • bwa_mem_Stats.log

Microbial Community Analysis in R

• MCA Analysis in phyloseq
  • phyloseq.Rmd

Resources

• Primer Design