CoGe

iPlant Data Store: Optional

• Keynote: http://de.iplantcollaborative.org/dl/d/C18C9F8A-12C6-4FB9-BAC6-001A55796DB8/2014_OSU_iPlant_Data_Store.key
• PDF: http://de.iplantcollaborative.org/dl/d/5D764133-5F54-4139-8D22-B6BD90B348C0/2014_OSU_iPlant_Data_Store.key.pdf
• iPlant user account: http://user.iplantcollaborative.org/
• iPlant Discovery Environment: https://de.iplantcollaborative.org/
• Data Store quick start: Guide
• iDrop:
  • Note:  iDrop is undergoing a series of updates to solve some problems with Java.  These link to a tested beta version that is MUCH better than the previous release.  If you visiting this page after Sept 2014, you should find a newer version:
  • iDrop MacOS: https://code.renci.org/gf/download/frsrelease/222/2488/iDrop_macos_2_0_1-beta3.dmg
  • iDrop Windows-x64: https://code.renci.org/gf/download/frsrelease/222/2491/iDrop_windows-x64_2_0_1-beta3.exe
  • iDrop Windows: https://code.renci.org/gf/download/frsrelease/222/2490/iDrop_windows_2_0_1-beta3.exe
  • iDrop Unix: https://code.renci.org/gf/download/frsrelease/222/2489/iDrop_unix_2_0_1-beta3.sh
• Using i-Commands: i-commands
  • Tips and tricks

CoGe

Slides:

• Keynote: http://de.iplantcollaborative.org/dl/d/CE840D14-E9BB-4CAE-A5C9-33F7D89DE0B8/2014_OSU_CoGe.key 
• PDF:http://de.iplantcollaborative.org/dl/d/C7A68B2E-4C7A-4A73-ABDF-143DD3B3398C/2014_OSU_CoGe.pdf

Comparative Genomics

• Human-Chimp whole genome: http://genomevolution.org/r/d76i
• Arabidopsis thaliana self-self: http://genomevolution.org/r/d7p5
• Arabidopsis thaliana v. Arabidopsis lyrata: http://genomevolution.org/r/d4hi
• Arabidopsis thaliana v. Arabidopsis lyrata (Synonymous values): http://genomevolution.org/r/d7e7
• 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
  • Send to SynFind: https://genomevolution.org/CoGe/SynFind.pl?fid=461399390
  • Search genome of Arabidopsis thaliana: http://genomevolution.org/r/d774
  • Microsynteny analysis: http://genomevolution.org/r/d778

 

Loading your own genome

• 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:

• Tutorials: https://genomevolution.org/wiki/index.php/Tutorials
• Arabidopsis/Brassica:  http://journal.frontiersin.org/Journal/10.3389/fpls.2012.00172/full
• Grasses (maize/sorghum): www.maydica.org/articles/56_183.pdf" class="external-link" rel="nofollow"linktype="raw" wikidestination="http://www.maydica.org/articles/56_183.pdf" originalalias="http://www.maydica.org/articles/56_183.pdf" >http://www.maydica.org/articles/56_183.pdf (http://

Additional Information

• iPlant Learning Center: http://www.iplantcollaborative.org/learning-center
• iPlant Data Store Quick Start
• iPlant: Using i-commands (command line access to the Data Store)

• Loading private data in CoGe: http://www.youtube.com/watch?v=JPZ8IrPnh_8
• RNASeq with EPIC-CoGe: https://www.youtube.com/watch?v=3fNyHGB02dM
• Paralogs and orthologs: http://www.annualreviews.org/doi/full/10.1146/annurev.genet.39.073003.114725?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed&#.U-J5WY1dV9k