User:Nbertin/CAGEscan driven annotation protocol

   CAGEscan paired-end data link TSSes to downstream sequences. By annotating those downstream sequence with respect to know transcript(s) and transcript feature(s) (exons, introns, UTRs) it is possible to extend the annotations of (HelicosCAGE derived) TSS or TC by comparing them to such annotated CAGEscan derived TSS. Note that his 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

• sample file
  
• script

CAGEscan-derived TSS annotation files

• <edit>

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

• Input

BED/OSCfile CAGE cluster
BED CAGEscan annotation file

• Output

Annotated CAGE cluster OSCfile