Data in the form of delimited text files is aggregated into [SQLShare](https://sqlshare.escience.washington.edu/sqlshare/) where they can be easily queried. The simplest way to start exploring the uses for this system is to interact with SQLShare using the simple web interface. All you need to get started is a Google account. [Please see this page for a beginner's guide to SQLshare](https://github.com/sr320/qdod/wiki/SQLShare-Intro).

There is a python client for advanced users.

Below is schematic representation of the different types of datasets.

<img src="https://github.com/sr320/qdod/blob/master/img/scheme.png?raw=true" width = 40%/>

Reference Genome Sequence files are described on [this page](https://github.com/sr320/qdod/wiki/Reference-Genome-Files).  

Currently the documentation is focused on 1) **describing current datasets** and 2) **providing workflow tutorials**.


####Raw Data

* [Select NGS Data via Roberts Lab](https://github.com/sr320/qdod/wiki/Roberts-Lab-Raw-Data)


####Datasets in SQLShare
* [Universal](https://github.com/sr320/qdod/wiki/Data-Snapshots#universal)
* [Generic Oyster Datasets](https://github.com/sr320/qdod/wiki/Data-Snapshots#general)
* [Tissue Specific Oyster Datasets](https://github.com/sr320/qdod/wiki/Data-Snapshots#tissue-specific)
* [v0.1 Datasets _archived_](https://docs.google.com/spreadsheet/pub?key=0AtV_gF766XZAdEVidTlESmRuZzdndG5tRUswQnRDQ0E&gid=0)


####Tutorials
* [Simple Gene Search](http://nbviewer.ipython.org/github/sr320/qdod/blob/master/search_ampk.ipynb)
* [Standard SQLShare Queries](https://github.com/sr320/qdod/wiki/Standard-Queries)
* [Annotating Genes](https://github.com/sr320/qdod/wiki/Workflow-1:-Annotating-Oyster-Genes)  
* [File Format Conversions](https://github.com/sr320/qdod/wiki/File-Format-Conversions)   

####Genome Browser Feature Tracks
* [Canonical Tracks](https://github.com/sr320/qdod/wiki/Genome-Feature-Tracks#canonical-feature-tracks)
* [Bisulfite sequencing (gill tissue)](https://github.com/sr320/qdod/wiki/Genome-Feature-Tracks#crassostrea-gigas-high-throughput-bisulfite-sequencing-gill-tissue)
* [Reference Genome Files](https://github.com/sr320/qdod/wiki/Reference-Genome-Files)

---

####List of Publications that use the qDOD framework
* Gavery MR and Roberts SB. (2013) [Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc](https://peerj.com/articles/215/) PeerJ 1:e215. doi:10.7717/peerj.215
* Olson CE and Roberts SB. (2014). [Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes](http://journal.frontiersin.org/Journal/10.3389/fphys.2014.00224/abstract) Frontiers in Physiology. 5:224. doi: 10.3389/fphys.2014.00224
([genome feature track](https://github.com/sr320/qdod/wiki/Genome-Feature-Tracks#crassostrea-gigas-high-throughput-bisulfite-sequencing-male-gamete))
* Timmins-Schiffman EB, Nunn BL, Goodlett DR and Roberts SB. (2013) [Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster](http://conphys.oxfordjournals.org/content/1/1/cot009.full.pdf+html) Conservation Physiology. doi:10.1093/conphys/cot009
* Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH et al. (2014) [Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas](http://dx.doi.org/10.7287/peerj.preprints.388v1). PeerJ PrePrints 2:e388v1 http://dx.doi.org/10.7287/peerj.preprints.388v1
* Olson, Claire; Roberts, Steven (2014): [Crassostrea gigas high-throughput bisulfite sequencing (larvae and sperm tissues)](http://figshare.com/articles/Crassostrea_gigas_high_throughput_bisulfite_sequencing_larvae_and_sperm_tissues_/1060465). figshare. http://dx.doi.org/10.6084/m9.figshare.1060465
* Olson, Claire; Roberts, Steven (2014): [Crassostrea gigas male gonad transcriptome data comparison](http://figshare.com/articles/Crassostrea_gigas_male_gonad_transcriptional_data_comparison/1004464). figshare. 
http://dx.doi.org/10.6084/m9.figshare.1004464
* Olson, Claire; Roberts, Steven; Gavery, Mackenzie (2013): [DNA methylation coverage in two tissues of the Pacific Oyster](http://figshare.com/articles/DNA_methylation_coverage_in_two_tissues_of_the_Pacific_Oyster/652964). figshare. 
http://dx.doi.org/10.6084/m9.figshare.652964
* Olson, Claire; Roberts, Steven; Gavery, Mackenzie (2013): [DNA Methylation Patterns in Crassostrea gigas](http://figshare.com/articles/NSA_Poster_2013_Claire_Ellis/478021). figshare. 
http://dx.doi.org/10.6084/m9.figshare.478021
* Gavery, Mackenzie; Roberts, Steven (2013): [Crassostrea gigas high-throughput bisulfite sequencing (gill tissue)](http://figshare.com/articles/Crassostrea_gigas_high_throughput_bisulfite_sequencing_gill_tissue_/749728). figshare. 
http://dx.doi.org/10.6084/m9.figshare.749728