EEB BootCamp 2020: Difference between revisions

From QiuLab
Jump to navigation Jump to search
imported>Weigang
imported>Weigang
Line 22: Line 22:


==Data set==
==Data set==
* Download file: [http://diverge.hunter.cuny.edu/~weigang/cov-camp.tar.gz data file]
* Download file: [http://diverge.hunter.cuny.edu/~weigang/qiu-akther.tar.gz data file]
* Create a directory, unzip, & un-tar
* Create a directory, unzip, & un-tar
<syntaxhighlight lang='bash'>
<syntaxhighlight lang='bash'>
Line 30: Line 30:
tar -tzf cov-camp.tar.gz # view files
tar -tzf cov-camp.tar.gz # view files
tar -xzf cov-camp.tar.gz # un-zip & un-tar
tar -xzf cov-camp.tar.gz # un-zip & un-tar
</syntaxhighlight>
* View files
<syntaxhighlight lang='bash'>
file TCS.jar
ls -lrt # long list, in reverse timeline
less Jan-Feb.mafft # an alignment of 565 CoV2 genomes in FASTA format; "q" to quit
less cov-565strains-617snvs.phy # non-gapped SNV alignment in PHYLIP format
wc hap.txt # geographic origins
head hap.txt
wc group.txt # color assignment
cat group.txt
less cov-565strains.gml # graph file (output)
</syntaxhighlight>
</syntaxhighlight>



Revision as of 07:08, 26 July 2020

Bioinformatics Boot Camp for Ecology & Evolution: Pathogen Evolutionary Genomics
Thursday, Aug 6, 2020, 2 - 3:30pm
Instructors: Dr Weigang Qiu & Ms Saymon Akther
Email: weigang@genectr.hunter.cuny.edu
Lab Website: http://diverge.hunter.cuny.edu/labwiki/
Lyme Disease (Borreliella) CoV Genome Tracker Coronavirus evolutuon
Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)
Spike protein alignment

Case studies from Qiu Lab

Data set

  • Download file: data file
  • Create a directory, unzip, & un-tar
mkdir QiuAkther
mv cov-camp.tar.gz QiuAkther/
cd QiuAkther
tar -tzf cov-camp.tar.gz # view files
tar -xzf cov-camp.tar.gz # un-zip & un-tar
  • View files
file TCS.jar
ls -lrt # long list, in reverse timeline
less Jan-Feb.mafft # an alignment of 565 CoV2 genomes in FASTA format; "q" to quit
less cov-565strains-617snvs.phy # non-gapped SNV alignment in PHYLIP format
wc hap.txt # geographic origins
head hap.txt
wc group.txt # color assignment
cat group.txt
less cov-565strains.gml # graph file (output)

Bioinformatics Tools & Learning Goals

Tutorial

  • 2-2:30: Introduction on pathogen phylogenomics
  • 2:30-2:45: data pre-processing with BpWrapper
  • 2:45-3:00: build haplotype network with TCS
  • 3:00-3:15: interactive visualization with BuTCS
  • 3:15-3:30: Q & A