Protocols:HeliScopeCAGE read alignment

The data sequenced on Heliscope sequencers are post processed, in order to:

• Discard the CAGE tags derived from the ribosomal DNA repeating unit, which is not contained in the genome assembly, by rRNAdust (developed by Timo Lassmann). See Protocols:rRNAdust
• Align the remained CAGE tags with the genome sequences with DELVE (developed by Timo Lassmann), which generate BAM files containing a single mapped position per read with mapping quality and alignments.
• Retain only those reads with mapping quality corresponding to a 99% accuracy.
• Aggregate the 5'-end of those mapped CAGE tags as CAGE transcription starting site (CTSS).