For reads mapping to multiple loci, upstream and downstream DNA sequences were obtained from one mapped site selected at random.
A drawback of the CAGE approach thus far has been the removal of as many as 40% of CAGE sequence tags due to their mapping to multiple genomic locations.
Sequences were discarded as mapping to multiple sites when they had more than one match on the human genome differing in identity less than 2%.
83.6% of all 15 bp SAGE tag sequences could be mapped to a single location in the 12 Mbp "giardia14" genome assembly, with an additional 9.0% mapping to multiple locations primarily due to duplicated genes.
In the latter file, probe sets whose consensus sequences mapped to one or no genomic positions receive mapping codes "SM" or "NM" respectively, and probe sets mapping to multiple positions are annotated with code "MM".
Only reads with under 384 CALs are subsequently evaluated by the powerful gapped local alignment algorithm, which distinguishes reads with identical mapping to multiple locations versus reads with a best matched location.
Mapping to multiple locations was permitted.
Probesets mapping to multiple genes were excluded.
Probes mapping to multiple gene identifiers are removed.
However, the frequency of degenerate peptides mapping to multiple clonotypes complicates this analysis.
Sequence reads with three mismatches or more and reads mapping to multiple positions were excluded.
