Protocols:HeliScopeCAGE read alignment
From FANTOM5_SSTAR
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)
- 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)
