Overview of 'DuffyTools' notion of Species
We use the notion of 'species' to mean a single organism or strain
that has it's own unique genomic annotation. Contrast this with
Our lab's focus is on host parasite interactions and most of our datasets involve measuring gene expression of both the host and the parasite in a single experiment, be it microarrays, proteomics, or NextGen sequencing. To accomplish this, we need to work with multiple species in a seamless and coordinated manner.
A species definition consists of a MapSet – a collection of objects that
completely describes the genomic annotation – and 2 unique identifiers:
a SpeciesID and a species FilePrefix. See
MapSets for full
details. The SpeciesID is used to tell the software which MapSet
(annotation) to use, and the FilePrefix is used for the reading and writing
of all species-specific files. Typically, the species file prefix is a
shortened version of the SpeciesID, unique over the set of all possible
species of interest.
In the trivial case of operating on datasets from just a single species, it is customary for the SpeciesID to exactly match the TargetID.
getCurrentGeneMap, to get the table of genes.
getCurrentExonMap, to get the table of coding exons.
getCurrentSeqMap, to get the table of sequences (chromosomes).
getCurrentRrnaMap, to get the table of ribosomal RNA and other
special case genes.
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