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 in
• 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

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

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

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