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Meanwhile, each read is labeled with its most likely origin based on comparing its mappings in multiple pseudogenomes.
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These data can be combined with statistical fine-mapping in multiple ways.
Extensions that were too short resulted in multiple mappings, and those that were too long produced no mapping.
They have the additional advantage of treating alternative transcripts and paralogous genes (resulting in multiple mappings for reads in genome alignment) naturally the same way.
We also show that these two sets of conditions are minimal in that removing any condition from each of them will result in multiple permissible mappings.
Given the limited scope of the MHAP project, the decision was made to allow for multiple mappings in cases where the matches, although not strictly equivalent, might nonetheless provide appropriate and valuable links between mouse and human data.
When a tRNA overlapped more than one mapping in another species, due to either low-resolution mappings or multiple mappings, orthology was preferentially assigned to a tRNA with the same identity and anticodon.
Mapping genetic variations causing differences in diverse healing responses in multiple tissues may reveal generic healing processes in pursuit of new therapeutic targets designed to induce or enhance regeneration and, potentially, protection from osteoarthritis.
Over the years, there have been attempts to support more complex mappings of multiple data values onto node visuals in Cytoscape.
Advances in multiple genomic platforms and analytical methods allow fine-mapping and cloning of QTL responsible for important agronomic traits [ 29].
MITIE can (i) take advantage of known transcripts, (ii) reconstruct and quantify transcripts simultaneously in multiple samples, and (iii) resolve the location of multi-mapping reads.
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