Annotation and Visualisation

Annotations
Additionally, Lace can provide three complementary annotations of these SuperTranscripts:

1) Annotation by Blocks: blocks are defined by matched overlapping parts of two or more of the transcripts which build the SuperTranscript, these are non-diverging paths on the graph. These blocks are thought of as exon-like structures, in reality they can include fewer or greater number of bases than one exon from annotated genome.

2) An annotation built from using the transcript coverage over the SuperTranscript. In other words, it annotates where the transcripts used to build the SuperTranscript map back to the SuperTranscript.

3) The final type of annotation one can build (which is subtly different than the block annotation), is to create an annotation based on the spliced read information. Once the SuperTranscript is constructed by mapping the reads back to it one can use split reads to infer the structure of common blocks.

Visualisation

The output of SuperTranscript is a fasta file and two annotation files (.gff). These can be easily read into the Integrative Genomics Viewer (IGV - https://www.broadinstitute.org/igv/) where one can easily view the read coverage of the SuperTranscript and the various annotations.

For example, one can use IGV to visualise DTU in a gene: