Revision as of 18:05, 8 September 2020

Fall 2020

Tuesdays at 12 noon - 2pm by Zoom
Sept 1, 2020. Week 1. Meet & Greet; Intro to projects
Sept 8, 2020. Week 2. Presentations (background, data, and methods), based on assigned readings

Participants: Desiree & Ramon
Readings
- Review: deCenzo & Finan (2017).
Data set: lp54 & cp26 plasmids
TO DO:
- Week 1. 9/8/2020, 12 noon: 5-slides presentation on multipartite bacterial genome evolution (based on the paper above)
- Week 2. 9/15, 12 noon: Use prorgram codonO to calculate codon bias (SCUO) for replicons (n=23) on Borrelia burgdorferi B31 genome

Participants: Justin, Roman
Readings: Ivanova et al (2009)
Tool: ImageJ
Data set (to be sent)
To Do
- Week 1. 9/8/2020 12 noon: 5-slide presentation on background, material & methods, and data capture using ImageJ
- Week 2. 9/15: Create Excel sheet to capture immunoblot intensities on C3H mice & P.lucus. Capture background for each serum. Getting ready to makes plots in R/Rstudio

Participants: Eaman, Zaheen
Readings
Data set: posted on "genometracker.org"
- Wild type transcriptome at 12 hour, paired-end read files:
- /home/azureuser/18134XR-29-01_S0_L001_R1_001.fastq.gz
- /home/azureuser/18134XR-29-01_S0_L001_R2_001.fastq.gz
To Do
- Week 1. 9/8/2020 12 noon:
  - A short presentation on C. diff transcriptome (one of the 2 papers above)
  - Demo on read quality using FastQC and mapping reads to reference genomes with bowtie
- Week 2. Use HT-Seq to quantify RNA abundance for C. diff genes

@@ Line 43: / Line 43: @@
 ** /home/azureuser/18134XR-29-01_S0_L001_R2_001.fastq.gz
 * To Do
-** 9/8/2020 12 noon:
+** Week 1. 9/8/2020 12 noon:
 *** A short presentation on C. diff transcriptome (one of the 2 papers above)
 *** Demo on read quality using FastQC and mapping reads to reference genomes with bowtie
+** Week 2. Use HT-Seq to quantify RNA abundance for C. diff genes
 ==Project 4. Protein classification using natural language processing==