Undergrad Research Experience: Difference between revisions
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*** [https://htseq.readthedocs.io/en/master/count.html Try this protocol first] | *** [https://htseq.readthedocs.io/en/master/count.html Try this protocol first] | ||
** Commands | ** Commands | ||
According to: [https://mmg434.readthedocs.io/en/latest/daythreemod.html reference] | According to: [https://mmg434.readthedocs.io/en/latest/daythreemod.html reference]; [http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#getting-started-with-bowtie-2-lambda-phage-example Bowtie website] | ||
<syntaxhighlight lang='bash'> | <syntaxhighlight lang='bash'> | ||
bioseq -i'genbank' R20291.gb > ref.fa # make FASTA file | bioseq -i'genbank' R20291.gb > ref.fa # make FASTA file | ||
bowtie2-build ref.fa index # build index | bowtie2-build ref.fa index # build index | ||
# -S: sam output (otherwise bam) -c: actual seqs, not file list | # -S: sam output (otherwise bam) -c: actual seqs, not file list | ||
bowtie2 -x index -1 ../18134XR-29-01_S0_L001_R1_001.fastq.gz -2 ../18134XR-29-01_S0_L001_R2_001.fastq.gz | bowtie2 -x index -S 18134XR.sam -1 ../18134XR-29-01_S0_L001_R1_001.fastq.gz -2 ../18134XR-29-01_S0_L001_R2_001.fastq.gz | ||
<syntaxhighlight> | <syntaxhighlight> | ||
Revision as of 18:13, 15 September 2020
Fall 2020
Participants
- Eamen Ho: Volunteer research assistant
- Ramandeep Singh: BIOL 48002
- Desiree Pante: BIOL 48001
- Afsana Rahman: Volunteer research assistant
- Roman Shimonov: BIOL 48002
- Justin Hiraldo: BIOL 48002
- Zaheen Hossain: Volunteer research assistant
- Jerry Sebastian: Volunteer research assistant
Schedule
- 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
Project 1. Structure & evolution of multipartite genome of Lyme disease bacteria
- Participants: Desiree & Ramon (Summer 2020), Jerry
- 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
- Week 3. 9/22, 12 noon: codonO paper presentation (Jerry)
Project 2. OspC Cross-reactivity analysis
- 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
Project 3. Clostridium transcriptome analysis
- 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.
- HTSeq installed
- Try this protocol first
- Commands
- Week 1. 9/8/2020 12 noon:
According to: reference; Bowtie website <syntaxhighlight lang='bash'> bioseq -i'genbank' R20291.gb > ref.fa # make FASTA file bowtie2-build ref.fa index # build index
- -S: sam output (otherwise bam) -c: actual seqs, not file list
bowtie2 -x index -S 18134XR.sam -1 ../18134XR-29-01_S0_L001_R1_001.fastq.gz -2 ../18134XR-29-01_S0_L001_R2_001.fastq.gz
<syntaxhighlight>
Project 4. Protein classification using natural language processing
- Participants: Afsana
- Goal: Classify protein sequences
- Week 1. 9/8/2020 Readings:
- Week 2. Find/Explore ALBERT resources & Tutorials