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Exact(6)
This script does not count any read that maps to more than one reference sequences, and multiple mappings to the same reference sequence are only counted once.
Most commonly, multiple mappings to the D. melanogaster genome occur for tRNAs located in clusters in D. melanogaster.
The computed GO-Motif association scores can be used to rank the multiple mappings to a GO term.
In the case of multiple IMS experiments and multiple mappings to the same atlas, one can compare the anatomical interpretations of multiple experiments to each other by using a common reference (atlas) space.
In a small number of cases, multiple mappings to a single location in D. melanogaster are observed; these signify duplications in the query species with respect to D. melanogaster and again often occur in clusters.
Since EFO is used to annotate data in ArrayExpress and also provides multiple mappings to other ontologies, it is possible to query data through BioPortal using ontology class names and return annotated data from multiple resources via the BioPortal's Resources facility, for example, pathway data from Reactome.
Similar(54)
Read fragments with multiple mappings (possibly to the same position) are passed to the Quality filter.
The decision to create multiple external mappings to EFO classes clearly presents additional overhead to both the initial set of mappings and the subsequent maintenance of these mappings, as both are labor intensive if performed manually.
Note that by doing so, a read with multiple mappings will contribute to the total read count of several transcripts.
The maximum number of read mismatches and read gap length were set to 2. Multiple mappings of single reads was set to 10 (default: 20) to decrease the bias for genes with more multimapping reads.
Multiple mappings show that flanking sequences map to regions of the D. melanogaster that are duplicated with respect to the query species.
Related(20)
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