2014 JCVI Summer Genomics Workshop

Talks

iPlant Data Store

• Keynote: http://de.iplantcollaborative.org/dl/d/32FB6BEE-D20B-42E7-BB3A-318BD55916C5/2014_JCVI_iPlant_Data_Store.key
• PDF: http://de.iplantcollaborative.org/dl/d/62D4D8BF-2233-4682-8FFD-A016590550F0/2014_JCVI_iPlant_Data_Store.key.pdf
• iPlant user account: http://user.iplantcollaborative.org/
• iPlant Discovery Environment: https://de.iplantcollaborative.org/
• Data Store quick start: https://pods.iplantcollaborative.org/wiki/display/start/Data+Store+Quick+Start
• Using i-Commands: https://pods.iplantcollaborative.org/wiki/display/start/Using+icommands

CoGe

• Keynote: http://de.iplantcollaborative.org/dl/d/51782D3C-3BCE-413D-BB30-6F2AB90CB1D7/2014_JCVI_CoGe.key
• PDF: http://de.iplantcollaborative.org/dl/d/AAA8B621-F80D-4D66-8080-81809B5D5639/2014_JCVI_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

Links

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

• Loading private data in CoGe: http://www.youtube.com/watch?v=JPZ8IrPnh_8
• RNASeq with EPIC-CoGe: https://www.youtube.com/watch?v=3fNyHGB02dM