Working with the Data

DeepBlue has the following commands for working with the data:

• select_regions — select experiment regions that match the given parameters
• select_annotations — select annotation regions that match the given parameters
• filter_regions — filter the regions
• intersection — return the regions that intersect the regions from another query
• merge_queries — merge two queries into one
• tiling_regions — create regions of the given tiling size over the chromosomes
• get_experiments_by_query — request experiment names and IDs of the selected regions
• count_regions — request the number of regions
• get_regions — request the query regions
• aggregate — get the regions for the given query in the requested BED format
• get_request_data - get the requested data
• info - get information about an entity or the data request

The usual workflow is: select the data with select_experiments and select_annotations. Next, filter the data with filter_regions or intersection. If necessary, select more data and merge them using the merge_queries. To view the results; it is possible to request the experiments containing selected data with the get_experiments_by_query, count_regions, or get_regions command (in the BED format), or in a data summary using aggregate. The status of the request can be viewed using info and the data retrieved using get_request_data.

The use of these commands will be explained in the following sections.