User:Nbertin/CAGEscan driven annotation protocol

   CAGEscan paired-end data link TSS to a downstream sequence. By annotating those downstream sequence with respect to know transcript feature (exon, intron, UTRs) it is possible to extend the annotations of (HelicosCAGE derived) TSS by comparing them to CAGEscan derived TSS. This can be accomplished either by comparing data arising from similar biological samples or comparing it to the full body of CAGEscan-derived TSS annotation files

CAGEscan-derived TSS annotation

CAGEscan-derived TSS annotation file construction

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CAGEscan-derived TSS annotation files

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Combining CAGEscan-derived TSS annotation files and (Helicos)CAGE clusters

• Input

BED/OSCfile CAGE cluster
BED CAGEscan annotation file

• Output

Annotated CAGE cluster OSCfile