2014 JCVI Summer Genomics Workshop: Difference between revisions

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==Talks==
==Sessions==


===iPlant Data Store===
===iPlant Data Store===
Keynote: http://de.iplantcollaborative.org/dl/d/32FB6BEE-D20B-42E7-BB3A-318BD55916C5/2014_JCVI_iPlant_Data_Store.key
* '''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
* '''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===
===CoGe===
Keynote: http://de.iplantcollaborative.org/dl/d/51782D3C-3BCE-413D-BB30-6F2AB90CB1D7/2014_JCVI_CoGe.key
* '''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


==Documentation==


iPlant Learning Center: http://www.iplantcollaborative.org/learning-center
====Loading your own genome====
iPlant Data Store Quick Start: https://pods.iplantcollaborative.org/wiki/display/start/Data+Store+Quick+Start
* 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


Loading private data in CoGe: http://www.youtube.com/watch?v=JPZ8IrPnh_8
* Arabidopsis RNA-Seq data: http://de.iplantcollaborative.org/dl/d/A7F5E57F-E776-46E0-9672-59264E663F8A/test_rna_seq_data_0.17M_reads.fastq
RNASeq with EPIC-CoGe: https://www.youtube.com/watch?v=3fNyHGB02dM


=Links=
==Additional Information==
 
* 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

Latest revision as of 12:52, 19 June 2014

Sessions

iPlant Data Store

CoGe

Comparative Genomics


Loading your own genome

Additional Information

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