This wiki serves as the _primary means for documentation_ for project qdod: **querying disparate oyster datasets**.

In brief, 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**.

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


B. 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)


C. 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)   

D. 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)

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Please use [GitHub's Issue feature](https://github.com/sr320/qdod/issues) to ask question, report problems, or suggest features.