SCANVIS - SCANVIS - a tool for SCoring, ANnotating and VISualizing splice
junctions
SCANVIS is a set of annotation-dependent tools for
analyzing splice junctions and their read support as
predetermined by an alignment tool of choice (for example, STAR
aligner). SCANVIS assesses each junction's relative read
support (RRS) by relating to the context of local split reads
aligning to annotated transcripts. SCANVIS also annotates each
splice junction by indicating whether the junction is supported
by annotation or not, and if not, what type of junction it is
(e.g. exon skipping, alternative 5' or 3' events, Novel Exons).
Unannotated junctions are also futher annotated by indicating
whether it induces a frame shift or not. SCANVIS includes a
visualization function to generate static sashimi-style plots
depicting relative read support and number of split reads using
arc thickness and arc heights, making it easy for users to spot
well-supported junctions. These plots also clearly delineate
unannotated junctions from annotated ones using designated
color schemes, and users can also highlight splice junctions of
choice. Variants and/or a read profile are also incoroporated
into the plot if the user supplies variants in bed format
and/or the BAM file. One further feature of the visualization
function is that users can submit multiple samples of a certain
disease or cohort to generate a single plot - this occurs via a
"merge" function wherein junction details over multiple samples
are merged to generate a single sashimi plot, which is useful
when contrasting cohorots (eg. disease vs control).