CAGEscan libraries are prepared using the nanoCAGE protocol OP-SOLEXA-nanoCAGE-Direct-v1.4, and sequenced paired-end according to standard procedures on Illumina Genome Analyzer IIx OP-Illumina-sequencing-PairedEnd-v3.0.
Post processing steps include:
- rRNA dust on ribosomal DNA repeating unit
- alignment of the CAGE reads with the genome
- 5'-end based aggregation of CAGE tags
These steps above are same as the ones for the HeliScope protocol.