modENCODE data and tools for the community Gos Micklem University of Cambridge www.modencode.org
Welcome message from author
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
modENCODE data and tools
for the community
Gos Micklem University of Cambridge
www.modencode.org
modENCODE DCC Data Flow modENCODE DCC data wranglers
submit data & meta-‐data
modENCODE DCC pipeline
QC vet
release
meta-‐data data
Faceted Browser modMine Amazon/Bionimbus
data.modencode.org intermine.modencode.org www.bionimbus.org 9p.modencode.org
modENCODE Data Volume
2317 of 3763 datasets released: ~6 TB
Final freeze: expect ~20-‐25 TB altogether
modENCODE Data Volume
2317 of 3763 datasets released: ~6 TB
Final freeze: expect ~20-‐25 TB altogether
Post-‐laptop era Nuisance to download
GEO/SRA (crude), WormBase/ FlyBase (refined) Amazon/ BioNimbus (all)
www.modencode.org
Faceted Browser: data.modencode.org
11
13
9p.modencode.org
14
GBrowse
Can save track combinations
www.modmine.org
www.modmine.org
- Antibody names: PolII, H3K4me1, CP190 - Lab names: Reinke, Snyder- Combine terms with AND/AND NOT: fly AND embryo
Growth
Chromatin preps
ChIP
Hybridisation
Scanning
Normalisation
Enriched regions
www.modmine.org
lists in modMine
fly gene expression from list
StaFsFcal enrichment GO terms PublicaFons
www.modmine.org
www.modmine.org
Science paperfigures
“amazon modENCODE data” hHp://aws.amazon.com/datasets/8042906995278110
42
NOTE: these snapshots only contained released data up to December 2011
AMI = Amazon Machine Image Mount everything, GBrowse, just data Pay as you go
43
www.bionimbus.org
Acknowledgments modENCODE DCC:
Nicole Washington, Seth Carbon, Ellen Kephart, Paul Lloyd, Chris Mungall, E.O. Stinson, Suzanna Lewis (LBNL)
Daniela Butano, Sergio Contrino, Fengyuan Hu, Rachel Lyne, Kim Rutherford, Richard Smith, Gos Micklem (Cambridge)
Angie Hinrichs, Jim Kent (UCSC)
Marc Perry, Peter Ruzanov, Quang Trinh, Zheng Zha, Lincoln Stein (OICR)
All the modENCODE data producers
Related Documents
