2018 LANGEBIO CINVESTAV: Intro to genome management and analysis with CoGe

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Workshop Presentation

https://bit.ly/2MCAVHF

Register an account/Log in

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  • Go to: http://user.cyverse.org
  • Register for a CyVerse account
    • CoGe uses CyVerse'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 CyVerse's Authentication Services.
    • After your CyVerse user registration is complete, you may need to activate CoGe as a service at https://user.cyverse.org/services/mine in order to have a special directory created in your CyVerse Data Store
  • Sign-in (link is in top-right of any CoGe page)
    • NOTE: This wiki (CoGePedia) uses a different authentication than CoGe!
  • Once your are logged in, you have access to "My Profile", CoGe's control page for all of your data and analyses.

Load your own genome

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If you are logged into CoGe with your user account, you can add new genomes to CoGe, keep them private, share them with collaborators, and make them fully public.

Small Genome (E. coli)

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  • 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)

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  • 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

If you have structural gene models for your genome, you can integrate them. While many tools can use the full genome, some tools (and some features) require having structural gene models (e.g., CDS).

Small genome (E. coli)

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  • Go to LoadAnnotation
  • The genome should automatically be loaded in LoadAnnotation
  • Set a version (e.g., "1")
  • Source: "CoGe" or "NCBI"
  • Press "Next"
  • Select "FTP/HTTP" Tab
  • Paste in link below:
  • Press "Next"
  • Review the data and associated information.
  • Press "Start Loading"
  • When the load is finished, pressing "Genome View" will launch the genome viewer (JBrowse).
  • Note: The length of time it takes to load annotations depends on the load on the database and the number of annotations being loaded. For this example (and no load on the server), it should take ~ 3-5 minutes.

Large genome (Arabidopsis thaliana)

Data Management

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CoGe lets you share private data with other users.

  • 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.


Find and visualize a genome

Comparative Genomic Analyses

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  • 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.

Comparative Genomics

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  • 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"

Blast

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CoGeBlast is CoGe's tool for blast sequences against any set of genomes in CoGe

Adding Experimental Data

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EPIC-CoGe is an extension to CoGe that lets you add any type of functional genomics and diversity data sets to CoGe.

  • Go to the detailed view for your E. Coli genome from the User Profile Page: https://genomevolution.org/CoGe/User.pl
  • Press "Load Experiment"
  • Note: This exercise will be loading expression data, variant data, and read alignment data. You can name your experiments appropriately
  • Add a name (e.g., "Expression: Treatment 1")
  • Add a description (e.g., "Generated by heat stress and RNASeq protocol 11B")
  • Add a version (e.g., "1")
  • Add a source (e.g., "CyVerse")
  • Leave restricted
  • Press Next
  • Select the "FTP/HTTP" tab
  • Paste in one of the following (based on what you've named your experiment)
  • Press "Get"
  • Press Next
  • CoGe should automatically detect the type of file, but you can always set it. The supported file types are available here
  • Press Next
  • The options presented depend on the detected file type. For these dataset, you can skip this step.
  • Press Next
  • Review the data and associated information.
  • Press "Start Loading" to start the loading the data.
  • When finished, there is a link to the experiment you loaded. From there, you can get detailed information on the experiment (and modify what you've entered) in ExperimentView
  • From ExperimentView, you can launch the genome browser by pressing "View"
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Visualizing data you just loaded

  • From your profile page, double click on the genome (or experiment) you loaded
  • Press "Browse". This will launch CoGe's implementation of JBrowse: GenomeView
  • You can select tracks to visualize in the menu on the right

RNASeq Processing

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EPIC-CoGe has a variety of pipelines for processing FastQ data. Its Expression Analysis Pipeline will clean your reads, map them, quantify their abundance to position in the genome, and quantify their abundance per transcript as FPKM values.

  • 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"
  • --OR--
  • Add experiment name: (e.g., "RNASeq-test")
  • Add description (optional)
  • Add version (1)
  • Add source (e.g., "coge")
  • Keep restricted
  • Search for "Col-0"
    • Make sure to select the version with genome ID 16911
  • Press "Next"
  • 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
  • Press "Next"
  • Leave the aligner set to "GSNAP" which is faster than Bowtie2
  • Leave read type to "single-end"
  • To use the Expression Analysis Pipeline, select the check-box next to "Enable"
    • For parameters on this test dataset, use the "CoGe Basic" method and set the minimum read depth to "1" (the example data is a subsample of a fastq file and contains 170,000 reads)
  • You can tell CoGe to automatically add the newly loaded data to a notebook by selecting the check-box next to "Add results to notebook"
  • You can tell CoGe to send you and email when the analysis is done by selecting the check-box next to "Send email when finished"
  • Press "Next"
  • Review the data and associated information.
  • Press "Start Loading" to start the analysis.
    • Note: Once the analysis starts running, you can close your browser.
    • Note: You can check on the status of your analysis by clicking on "Data Loading" under "Activity" in your Profile Page
  • 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 (if selected) with three experiments as well provide links to each experiment.
    • 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)
  • You can find your newly loaded experiments by clicking on "Experiments" under "My Data"
    • From there, you can double click on the experiment to get information about it along with links to visualize the data in JBrowse

SNP and Variant Detection

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You can identify SNPs/variants in CoGe by following the RNASeq processing tutorial, but selecting to enable SNP Identification

  • Details on the SNP processing pipeline are found here

Data files reference

CoGe Learning Material

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