@article{
 title = {A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE},
 type = {article},
 year = {2008},
 identifiers = {[object Object]},
 pages = {281-288},
 volume = {91},
 id = {433801af-f95b-3431-b39f-6b8dd077fbf5},
 created = {2017-02-22T12:54:27.000Z},
 accessed = {2017-02-11},
 file_attached = {true},
 profile_id = {106bc146-844a-328b-bf78-76e2f9dc2912},
 group_id = {a235666b-677f-3998-90e9-3e538c744d39},
 last_modified = {2017-02-22T12:54:28.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 abstract = {Cap analysis gene expression (CAGE) is a high-throughput, tag-based method designed to survey the 5′ end of capped full-length cDNAs. CAGE has previously been used to define global transcription start site usage and monitor gene activity in mammals. 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. Here, we address the origins of multimap tags and present a novel strategy to assign CAGE tags to their most likely source promoter region. When this approach was applied to the FANTOM3 CAGE libraries, the percentage of protein-coding mouse transcriptional frameworks detected by CAGE improved from 42.9 to 57.8% (an increase of 5516 frameworks) with no reduction in CAGE to microarray correlation. These results suggest that the multimap tags produced by high-throughput, short sequence tag-based approaches can be rescued to augment greatly the transcriptome coverage provided by single-map tags alone.},
 bibtype = {article},
 author = {Faulkner, Geoffrey J. and Forrest, Alistair R.R. and Chalk, Alistair M. and Schroder, Kate and Hayashizaki, Yoshihide and Carninci, Piero and Hume, David A. and Grimmond, Sean M.},
 journal = {Genomics},
 number = {3}
}

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