2015 PAG Computer Demo: Difference between revisions
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===Register an account/Log in=== | ===Register an account/Log in=== | ||
*Go to: http://user.iplantcollaborative.org | *Go to: http://user.iplantcollaborative.org | ||
**CoGe uses iPlant's Authentication and User Identify Management | **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) | *Sign-in (link is in top-right of any CoGe page) | ||
*'''NOTE:''' This wiki (CoGePedia) uses a different authentication than CoGe! | *'''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=== | ===Comparative Genomics=== | ||
Revision as of 21:36, 5 January 2015
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