2014 JCVI Summer Genomics Workshop: Difference between revisions

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Revision as of 12:51, 19 June 2014

Sessions

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

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

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