There will be five sessions spread of 2.5 days. Sessions 1-3 will be coducted by EDACC staff. Session 4 will be conducted by REMC and disease project representatives. Session 5 will focus on potential collaborative projects between EDACC and other NIH Epigenomics Roadmap Initiative members.
The workshop will include 3 exercises (as part of Sessions 1-3). The following data generated by the consortium may be used for the exercises:
|H1 cell line||IMR90 cell line|
Thursday, Sep 10th
|Session 1: Data Flow and Genboree
This session will have dual focus: (a) Epigenomic Data Flow and (b) Introduction to Genboree
|Opening and Introduction – Art Beaudet and Aleks Milosavljevic
Data flow overview – Aleks Milosavljevic
Metadata, raw and analysis data, data flow
|10:00am-10:30am||Genboree feature overview – Alan Harris
Databases, tracks, projects, groups, users, access control
|10:45am-12noon||Genboree Exercises – Alan Harris|
Session 2: Primary Data and Pipelines ( Galaxy and Genboree integration, Tools)
This session will have dual focus: (a) Primary data Analysis and (b) Galaxy/Genboree integration
|1:00pm-1:30pm||Galaxy-Genboree integration – Alan Harris
Integration of Galaxy pipelines and Genboree via Genboree APIs
|1:30pm-2:15pm||Primary Data Analysis Pipelines – Cristi Coarfa
Read mapping via Pash. Defining and computing Level 2, 3 data for various assays and pipelines. Defining verification procedures.
|2:15pm-3:45pm||Primary Data Analysis Exercises – Cristi Coarfa
Running Genboree-integrated EDACC-hosted Galaxy reference pipelines to perform primary analysis for various assays.
|4:00pm-5:00pm||Data Analysis Tools – Wei Li
MACS, BS-seq, others.
|5:00pm-6:00pm||EDACC Housewarming party (Suite 400D)|
|6:30pm-8:00pm Dinner||(Trevisio restaurant, Texas Medical Center)|
Friday, Sep 11th
|Session 3: Integrative Data Analysis and Visualization and Genboree APIs
This session will have dual focus: (a) Integrative Data Analysis and (b) EDACC-hosted methods and tools relevant of Intregrative Analysis: Virtual Genome Painting and Genboree APIs
|9:00am-10:00am||Integrative Data Analysis and Visualization – Cristi Coarfa
Finding differenecs: ChIP-seq, MACs and multiscale. Visualization in the context of UCSC tracks ( by using UCSC service or Genboree warehousing )
|10:00am-10:15am||Integrative Data Analysis and Visualization Exercises – Cristi
Virtual Genome Painting, Circos.
|11:00am-12noon||Using Genboree APIs to retrieve integrated data sets– Andrew Jackson
Retrieving data for integrative analysis of multiple marks, clustering and heatmap visualization.
|Session 4: Participant-supplied topics: problems, solutions, and opportunities addressable in collaboration between REMCs or disease-focused projects and EDACC|
A sampling of problems/solutions/opportunities that may be addressed:
1. Sharing pre-publication data among members of collaboratring groups. Examples: sharing pre-publication data generated by REMCs among REMCs; sharing pre-publication data generated by disease projects among disease projects.
2. Pash mapping service for all assays ( EDACC automatically generating upon REMC data submission Level 1 data in SAM format for all assays )
3. Developement of reference pipelines: defining and computing Level 2, 3 data for all assays
4. Defining verification procedures and coordinating REMCs verfication and EDACC verification.
5. Defining epigenome similarity measures (multiscale) to identify global/local similarities and differences.
6. Warehousing external epigenomic and other data sets of relevance for integrative analysis
7. Developing, integrating, and serving up visualization tools: VGP, Circos, heatmaps, others
8. Integrative analysis: Serving up integrated data sets via Genboree APIs
|1:15pm-1:45pm||UW: Bob Thurman|
|Multiscale analysis, chipseq and chromatin accessibility.|
|Histone modification marks algorithms and analysis
|2:15pm-2:45pm||UCSD: Lee Edsall|
|Comparing lanes, peak calling, bisulfite sequencing mapping.|
|2:45pm-3:15pm||Broad: Noam Shoresh|
|Discussion of topics of interest rather than a presentation. Peak calling, segmentation, analysis issues.|
Saturday, Sep 12th
|Session 5: Outline of potential collaborative projects|
|9:00am-9:45am||Outline of Collaborative Project 1|
|9:45am-10:30am||Outline of Collaborative Project 2|
|10:45am-11:30am||Outline of Collaborative Project 3|
|11:30am-12:00noon||Closing Remarks and Adjourn – Aleks Milosavljevic|