Difference between revisions of "How to load genomes into CoGe"

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(Created page with 'There are two general programs to run: *'''fasta_genome_loader.pl'': **Loads in fasta sequences into CoGe *annotation loader: **usually some version of '''gff_annotation_loader.p...')
 
 
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There are two general programs to run:
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You can load your own genome sequence, annotation, and quantitative data for use with CoGe's tools. These data may be kept private and shared with collaborators, or made fully public.
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*'''fasta_genome_loader.pl'':
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**Loads in fasta sequences into CoGe
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*annotation loader:
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**usually some version of '''gff_annotation_loader.pl''' or some other program for loading text based gene models and annotations
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#Register for a CyVerse user account if you don't have one:  https://user.cyverse.org
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==UAGC Example==
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## Add CoGe as a CyVerse Service:
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The UAGC produces many genomic sequences.  This is to help them streamline their procedure for loading genomes into CoGe
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## [[File:Screen Shot 2017-08-14 at 3.41.40 PM.png|400px]]
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#Get 454AllContigs.fna
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#Log into CoGe: https://genomevolution.org
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##This is the usual contig-level genome assembly from the 454 genome sequencing pipeline
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## [[File:Screen Shot 2020-05-28 at 8.52.36 AM.png|400px]]
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#run fasta_genome_loader.pl
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#Go to your [[User|User Profile Page]] by clicking My Data in the menu bar.
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  ~/projects/CoGeX/scripts/fasta_genome_loader.pl \
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## [[File:Screen Shot 2020-05-28 at 8.54.09 AM.png|400px]]
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-org_name "Acidovorax sp. strain JS42 substrain KSJ2" \
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#Click '''New''' -> '''New Genome'''
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-org_desc "Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Acidovorax;" \
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##[[File:Screen Shot 2020-05-28 at 8.54.30 AM.png|400px]]
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-source_name "University of Arizona Genetics Core" \
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# Follow [[LoadGenome|this link]] for information on how to use [[LoadGenome]].  
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-source_link "http://uagc.arl.arizona.edu/" \
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## Once your genome is loaded into the system, you can add annotation and quantitative data to it using the [[LoadAnnotation]] and [[LoadExperiment]] features.
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-ds_version .1 \
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#'''Note:''' Make sure your GFF file is in the correct format for CoGe: [[GFF ingestion]]
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-nt KSJ2_454AllContigs.fna \
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#If you get an error when accessing the CyVerse Data Store, make sure that CoGe has been added as a service to your CyVerse account: https://user.cyverse.org
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  -dsg_restricted 1
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## [[File:Screen Shot 2017-08-14 at 3.41.40 PM.png|400px]]

Latest revision as of 09:38, 28 May 2020

You can load your own genome sequence, annotation, and quantitative data for use with CoGe's tools. These data may be kept private and shared with collaborators, or made fully public.

  1. Register for a CyVerse user account if you don't have one: https://user.cyverse.org
    1. Add CoGe as a CyVerse Service:
    2. Screen Shot 2017-08-14 at 3.41.40 PM.png
  2. Log into CoGe: https://genomevolution.org
    1. Screen Shot 2020-05-28 at 8.52.36 AM.png
  3. Go to your User Profile Page by clicking My Data in the menu bar.
    1. Screen Shot 2020-05-28 at 8.54.09 AM.png
  4. Click New -> New Genome
    1. Screen Shot 2020-05-28 at 8.54.30 AM.png
  5. Follow this link for information on how to use LoadGenome.
    1. Once your genome is loaded into the system, you can add annotation and quantitative data to it using the LoadAnnotation and LoadExperiment features.
  6. Note: Make sure your GFF file is in the correct format for CoGe: GFF ingestion
  7. If you get an error when accessing the CyVerse Data Store, make sure that CoGe has been added as a service to your CyVerse account: https://user.cyverse.org
    1. Screen Shot 2017-08-14 at 3.41.40 PM.png
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