Help:How do I retrieve oligo data

From VectorBase Help System

[edit] BioMart

The easiest way to get all the oligo data for Anopheles gambiae is using BioMart.

BioMart will retrieve the transcripts to which ann oligo is associated.

Go to http://www.biomart.org
Click on MARTVIEW
Select "ENSEMBL GENES (SANGER)" as the Database
Choose "Anopheles gambiae genes (AgamP3)" as the Dataset
That'll get you started with the Anopheles genes.
The oligos are listed under "attributes".
Click on "Attributes" on the left.
Click on the "EXTERNAL" Expansion plus sign.
In the "Microarray Attributes" section, check the microarrays you are interested in.
Click on Results in the upper left, that'll give you all the GeneIDs and associated oligos.
After the results are pulled up, you can export the data to file in a variety of formats.

[edit] API

More complicated but allow more detailed queries such as getting the raw alignments of the oligo probes against the genome. Refer to the API documentation or e-mail help@vectorbase.org for more details about a specific query. Below is a brief description of where to find which data type.

The mapping of the probes to the transcripts is done in 2 steps:

STEP-1: Map all the probes to the genome (*oligo* tables)
- oligo_array: list of arrays that have been mapped to the transcripts (eg: Affymetrix array)
- oligo_probe: list of the probes composing each array
- oligo_feature: 'raw' match of each probe to the genome

Note that for the Affymetrix arrays, the probes are groups in sets (11 probes per set).

Each set was designed to map to a single transcript but this was done on the very first Anopheles gene set and might not be the case an more.

STEP-2: Then map the probes to the transcript(s) (*xref* tables)
- xref: list of possible 'entities' to map to a transcript/protein
- identity_xref: link the 'entity' (= xref) to a transcript/protein (= ensembl_object)
- object_xref: match of the 'entity' (xref) to the transcript/protein