2015 PAG Computer Demo

Slides

• Keynote:
• PDF:

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

• Start:
  • From your user profile page (must be logged into CoGe): https://genomevolution.org/CoGe/User.pl
    • Click "Create"-> "New Genome"
    • Go directly to LoadGenome: https://genomevolution.org/CoGe/LoadGenome.pl
• 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 "Add Data"
• Select "FTP/HTTP" tab
• Paste in the link below:
  • E. coli genome: http://de.iplantcollaborative.org/dl/d/555B53F9-E738-4951-85A3-421E23804DFA/genome_7112.faa
• Press "Get"
• When finished being retrieved, press "Load Genome"
• 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.

Add Annotations

• Go to GenomeInfo by pressing "View Genome"
• Press "Load Gene Annotations"
• Set a version (e.g., "1")
• Source: "CoGe" or "NCBI"
• Leave Restricted
• Press "Select Data Files"
• Select "FTP/HTTP" Tab
• Paste in link below:
  • E. coli annotations: http://de.iplantcollaborative.org/dl/d/C1ACC5C3-1E0B-409B-8A91-C969943F41F8/7122-structural-annotations.gff
  • Press "Get"
  • When finished being retrieved, press "Load Annotations"
• 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.

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

• 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., "iPlant")
• Leave restricted
• Press "Select Data File"
• Select the "FTP/HTTP" tab
• Paste in one of the following (based on what you've named your experiment)
  • E. coli expression data: http://de.iplantcollaborative.org/dl/d/F1EE1A86-F91A-46E7-92D6-A25EE78E3DA3/7112-lo.csv
  • E. coli variant data: http://de.iplantcollaborative.org/dl/d/B4040AC9-74A7-4E3E-B074-F23E1D70823E/7112-demo.vcf.gz
  • E. coli bam read alignment data: http://de.iplantcollaborative.org/dl/d/D0FC54E4-6DA6-4604-BE19-81F1D33B5350/7112-alignment.bam
• Press "Get"
• Select the type of data file:
  • Expression data are: CVS
  • Variant data are: VCF
  • Read alignments are: BAM
• Press "Load Experiment" when read to load data
• When finished, 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"

Comparative Genomics

• Human-Chimp whole genome: http://genomevolution.org/r/d76i
  • Go to SynMap: https://genomevolution.org/CoGe/SynMap.pl
  • Search for "human" and "chimp" in each of the Organism search boxes.
  • Select the "Display Options" tab and "Sort Chromosomes" by "Name"
  • Press "Generate SynMap"

• Arabidopsis thaliana self-self: http://genomevolution.org/r/d7p5
  • Go to SynMap: https://genomevolution.org/CoGe/SynMap.pl
  • Search for "Col-0" in both of the Organism search boxes
  • Note: many people are making copies of Arabidopsis Col-0 -- select the one with genome ID 16911
  • Press "Generate SynMap"

• Arabidopsis thaliana v. Arabidopsis lyrata: http://genomevolution.org/r/d4hi
  • Go to SynMap: https://genomevolution.org/CoGe/SynMap.pl
  • Search for "Col-0" and "lyrata" in each of the Organism search boxes.
  • Press "Generate SynMap"

• 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"

• SynFind
  • Find a peach gene in the genome browser: https://genomevolution.org/CoGe/GenomeView.pl?chr=scaffold_1&gid=22743&x=10266537&z=6&loc=scaffold_1%3A10266380..10666380&tracks=sequence%2Cfeatures
  • Click on a peach gene to get detailed information about it. This includes links to tools in CoGe for downstream analysis
  • Send to SynFind by clicking on "SynFind" next to "CoGe Links" : https://genomevolution.org/CoGe/SynFind.pl?fid=461399390
    • Note: SynFind is CoGe's tool for identify syntenic regions in any number of other genomes using a gene to anchor your location in a query genome. This tool only works on genomes with CDS annotations.
  • Search and add the genome of Arabidopsis thaliana Col-0: http://genomevolution.org/r/d774
    • Search for "Col-0" in the Organism search box
    • Select the TAIR genome (id 16911)
    • Add the Arabidopsis genome by pressing the "Add" button
    • Run SynFind by pressing "Run SynFind"
  • Microsynteny analysis: http://genomevolution.org/r/d778

RNASeq Processing

• Arabidopsis RNA-Seq data: http://de.iplantcollaborative.org/dl/d/A7F5E57F-E776-46E0-9672-59264E663F8A/test_rna_seq_data_0.17M_reads.fastq

Data files reference

• E. coli genome: http://de.iplantcollaborative.org/dl/d/555B53F9-E738-4951-85A3-421E23804DFA/genome_7112.faa
• E. coli annotations: http://de.iplantcollaborative.org/dl/d/C1ACC5C3-1E0B-409B-8A91-C969943F41F8/7122-structural-annotations.gff
• E. coli expression data: http://de.iplantcollaborative.org/dl/d/F1EE1A86-F91A-46E7-92D6-A25EE78E3DA3/7112-lo.csv
• E. coli variant data: http://de.iplantcollaborative.org/dl/d/B4040AC9-74A7-4E3E-B074-F23E1D70823E/7112-demo.vcf.gz
• E. coli bam alignment data: http://de.iplantcollaborative.org/dl/d/D0FC54E4-6DA6-4604-BE19-81F1D33B5350/7112-alignment.bam
• Arabidopsis RNA-Seq data: http://de.iplantcollaborative.org/dl/d/A7F5E57F-E776-46E0-9672-59264E663F8A/test_rna_seq_data_0.17M_reads.fastq

CoGe Learning Material

• Loading private data in CoGe: http://www.youtube.com/watch?v=JPZ8IrPnh_8
• RNASeq with EPIC-CoGe: https://www.youtube.com/watch?v=3fNyHGB02dM
• Tutorials: https://genomevolution.org/wiki/index.php/Tutorials
• Arabidopsis/Brassica: http://journal.frontiersin.org/Journal/10.3389/fpls.2012.00172/full
• Grasses (maize/sorghum): http://www.maydica.org/articles/56_183.pdf