2015 Plant Genome Evolution Workshop

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Slides

  • Keynote:
  • PDF:
  • Powerpoint:

Register an account/Log in

  • Go to: http://user.iplantcollaborative.org
    • CoGe uses iPlant's Authentication and User Identify Management Service
    • After clicking on the confirmation link provided in the automated email, your account may take a few minutes to propagate to all of iPlant's Authentication Services.
  • Sign-in (link is in top-right of any CoGe page)
  • NOTE: This wiki (CoGePedia) uses a different authentication than CoGe!

Load your own genome

Small Genome (E. coli)

  • Search for Organism "Escherichia coli K12 strain K-12 substrain MG1655" (just type in "MG1655")
  • Set a version (e.g., "1")
  • Leave "Type:" as "unmasked"
  • Source: "CoGe" or "NCBI"
  • Leave as "Restricted"
  • Press "Next"
  • Select "FTP/HTTP" tab
  • Paste in the link below:
  • Press "Get"
  • Press "Next"
  • Review the data and associated information.
  • Press "Start Loading"
  • Note: The length of time it takes to load a genome depends on the load on the database and the number of chromosomes/contigs being loaded. For this example, it should take a minute or two.
  • Note: When finished, you can select what you want to do next from a drop-down menu:
    • Go to GenomeInfo
    • Load Annotations for the genome
    • Load Another Genome

Medium Genome (Arabidopsis thaliana)

  • Search for Organism "Arabidopsis thaliana Col-0 (thale cress)" (just type in "col-0")
  • Set a version (e.g., "1")
  • Leave "Type:" as "unmasked"
  • Source: "CoGe" or "TAIR"
  • Leave as "Restricted"
  • Press "Next"
  • Select "FTP/HTTP" tab
  • Paste in the link below:
  • Press "Get"
  • Press "Next"
  • Review the data and associated information.
  • Press "Start Loading"
  • Note: The length of time it takes to load a genome depends on the load on the database and the number of chromosomes/contigs being loaded. For this example, it should take a minute or two.
  • Note: When finished, you can select what you want to do next from a drop-down menu:
    • Go to GenomeInfo
    • Load Annotations for the genome
    • Load Another Genome

Add Annotations (E. coli)

Add Annotations (Arabidopsis thaliana)

Find and visualize a genome



Data Management

  • Go to your User Profile page: https://genomevolution.org/CoGe/User.pl
  • Select a genome by clicking on it.
  • Information about the genome will appear in the right panel
  • You can share a genome by clicking on the person icon
  • You can delete the genome by clicking on the trash can
  • Double-clicking the genome will open the Detailed View for it (GenomeInfo)
  • Share it with the person next to you
  • You can view genomes (and other data) that has been shared with you by clicking on "Shared with me" in the menu on the left.

Analyses

  • Get the detailed view of your genome (GenomeInfo)
  • Under "Tools" and next to "Analyze", click on the link for "SynMap"
  • Your genome will automatically be populated for both genomes
  • Search for another E. coli genome by typing "MG1655" into one of the Organism search boxes
    • The one auto-select from that search will be perfect for the analysis (ID 4242)
  • Scroll to the bottom of the page and press the red button "Generate SynMap"
  • When the analysis is finished, press "Go" to see the results
  • Click on the dotpot to get a zoomed-in version of the dotplot.
  • Scroll onto the green line in the dotplot and double click when the cross-hairs turn red to launch GEvo for microsynteny analysis
  • Press "Run GEvo" to run GEvo
  • Note: This link will run a SynMap analysis for E. coli K12 substrains MG1655 and DH10B: https://genomevolution.org/r/daqz

Your History and Activity

  • If you are logged into CoGe, CoGe will record your activities. These are available for review in your User Profile page: https://genomevolution.org/CoGe/User.pl
  • Click on "Activity" in the menu on the left. This will give you an overview of the number of analyses you've run
  • Your previously run analyses can be viewed by clicking "Analyses". Clicking on an analysis will re-run it.
  • Your previously loaded data can be viewed by clicking "Data loading". Clicking on a previously loaded data will open the detailed view for those data.

Adding Experimental Data

Comparative Genomics

  • Arabidopsis thaliana v. Arabidopsis lyrata (Synonymous values): http://genomevolution.org/r/d7e7
    • Go to SynMap: https://genomevolution.org/CoGe/SynMap.pl
    • Search for "Col-0" and "lyrata" in each of the Organism search boxes.
    • Select the "Analysis Options" tab near the top of the screen
    • Under "CodeML" and next to "Calculate syntenic CDS pairs and color dots", select "Synonymous (Ks)"
    • Press "Generate SynMap"

RNASeq Processing

  • Note: You can add private experimental data to public genomes (Mix and match public and private data)
  • Go to your User Profile page: https://genomevolution.org/coge/User.pl
  • Select "Create" -> "New Experiment"
  • Add experiment name: (e.g., "RNASeq-test")
  • Add description
  • Add version
  • Add source (e.g., "coge")
  • Keep restricted
  • Search for "Col-0"
    • Make sure to select the version with genome ID 16911
  • Press "Select Data File"
  • Select the "FTP/HTTP" tab
  • Copy in the following link:
  • Press "Get"
  • It will automatically detect that it is a fastq file based on the file name extension
  • Leave the aligner set to "GSNAP" which is faster than Bowtie2
  • Press "Load Experiment"
    • Note: This Fastq file is relatively small and the whole pipeline takes around 2-3 minutes to complete
  • When finished, Load Experiment will create a notebook with three experiments
    • One for the BAM file (alignment)
    • One for reads mapped to nucleotide positions in the genome (read depth)
    • One for reads normalized to transcripts (FPKM)
  • Press "Notebook View" to view the notebook with all three experiments
  • Press "View" to visualize these data in the genome browser (JBrowse)
    • Due to the number of experiments (public) available for Arabidopsis Col-0, it may take JBrowse a while to load.

Data files reference

CoGe Learning Material

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