Difference between revisions of "2015 PAG Computer Demo"

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===Slides===
 
===Slides===
* '''Keynote:'''  
+
* '''Keynote:''' http://de.iplantcollaborative.org/dl/d/9DC49878-2818-4805-88F9-8337119036D4/2015-PAG-CoGe-Computer-Demo.key
* '''PDF''':  
+
* '''PDF''': http://de.iplantcollaborative.org/dl/d/427C0DD5-E7AB-4FA4-92D5-926F83C390C2/2015-PAG-CoGe-Computer-Demo.pdf
 +
* '''Powerpoint''': http://de.iplantcollaborative.org/dl/d/FA1A67DC-EEDA-4F11-802E-9B39B414BE01/2015-PAG-CoGe-Computer-Demo.pptx
  
 
===Register an account/Log in===
 
===Register an account/Log in===
 
*Go to: http://user.iplantcollaborative.org
 
*Go to: http://user.iplantcollaborative.org
**CoGe uses iPlant's Authentication and User Identify Management Sercice
+
**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)
 
*Sign-in (link is in top-right of any CoGe page)
 
*'''NOTE:''' This wiki (CoGePedia) uses a different authentication than CoGe!
 
*'''NOTE:''' This wiki (CoGePedia) uses a different authentication than CoGe!
 +
 +
===Find and visualize a genome===
 +
* Find a genome using [[OrganismView]]
 +
** Search for E. coli MG1655 my typing "MG1655" in the search box
 +
** E. coli MG1655: https://genomevolution.org/CoGe/OrganismView.pl?oid=24290
 +
* Detailed Genome Information in [[GenomeInfo]]
 +
** Follow the link to GenomeInfo under "Genome Information"
 +
** E. coli MG1655: https://genomevolution.org/CoGe/GenomeInfo.pl?gid=4242
 +
* Visualize Genome in [[GenomeView]]
 +
** View the genome in the genome browser by pressing the "View" button
 +
** E. coli MG1655: https://genomevolution.org/CoGe/GenomeView.pl?gid=4242
 +
 +
===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===
 
===Comparative Genomics===
 
* Human-Chimp whole genome: http://genomevolution.org/r/d76i
 
* 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
 
* 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
 
* 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
 
* 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
 
*SynFind
** Find a peach gene: https://genomevolution.org/CoGe/GenomeView.pl?chr=scaffold_1&gid=22743&x=10266537&z=6&loc=scaffold_1%3A10266380..10666380&tracks=sequence%2Cfeatures
+
** 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
** Send to SynFind: https://genomevolution.org/CoGe/SynFind.pl?fid=461399390
+
** Click on a peach gene to get detailed information about it.  This includes links to tools in CoGe for downstream analysis
** Search genome of Arabidopsis thaliana: http://genomevolution.org/r/d774
+
** 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"
 +
*** When the results are returned, there is a link to analyze the identified syntenic regions with GEvo to confirm synteny.
 
** Microsynteny analysis: http://genomevolution.org/r/d778
 
** Microsynteny analysis: http://genomevolution.org/r/d778
+
 
===Loading your own genome===
+
===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:
 +
** Arabidopsis RNA-Seq data: http://de.iplantcollaborative.org/dl/d/A7F5E57F-E776-46E0-9672-59264E663F8A/test_rna_seq_data_0.17M_reads.fastq
 +
* 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===
 
* E. coli genome:  http://de.iplantcollaborative.org/dl/d/555B53F9-E738-4951-85A3-421E23804DFA/genome_7112.faa
 
* 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 annotations: http://de.iplantcollaborative.org/dl/d/C1ACC5C3-1E0B-409B-8A91-C969943F41F8/7122-structural-annotations.gff
Line 26: Line 182:
 
* E. coli variant data: http://de.iplantcollaborative.org/dl/d/B4040AC9-74A7-4E3E-B074-F23E1D70823E/7112-demo.vcf.gz
 
* 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
 
* E. coli bam alignment data: http://de.iplantcollaborative.org/dl/d/D0FC54E4-6DA6-4604-BE19-81F1D33B5350/7112-alignment.bam
 
===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
 
* Arabidopsis RNA-Seq data: http://de.iplantcollaborative.org/dl/d/A7F5E57F-E776-46E0-9672-59264E663F8A/test_rna_seq_data_0.17M_reads.fastq
  

Latest revision as of 17:30, 6 January 2015

Slides

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!

Find and visualize a genome

Load your own genome

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:
  • 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

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