Slinker is a superTranscript generation and visualisation method. Slinker builds on the concept of visualisation using superTranscripts, but uses genome-guided assembly rather than predefined annotation to incorporate the novel transcribed regions of interest into a reference. Through this, Slinker retains novel transcribed regions outside of annotated exons such as novel exons, retained introns, alternate splicing, truncated exons, and extended exons.

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Genomic events often reverberate through to the transcriptome. Through these events gene products can be inhibited, upregulated, or modified in such a way as to disrupt typical function. Therefore, understanding how a genomic variant has altered transcription can potentially offer insight into a causal mechanism for pathogenesis or potential targets for therapeutic intervention.

So what CAN happen when we have an altered transcript? Lots of things! Many of which are outlined in Marek Cmero's fine cryptic variant caller, MINTIE. But a very interesting subset are "Novel Splice Variants", depicted in Figure 2 of Marek's paper and below. These variants can alter the post-transcriptional splicing of a transcript to: extend an exon, retain an intron, include a "novel" exon, truncate exons, or skip them entirely.

Well, sorry... That's a bit tricky! You see, what is typically done is that we align our RNA-Seq to the reference genome. As these reads are highly more likely to align to exons than introns we will see very sparse visualisations as a result. This is due to exons being far smaller than introns.

The Oshlack Lab developed the superTranscript as a method around this. The idea is simple but the result is powerful. Basically, we take all of the reference transcripts, remove the introns and concatenate the exons together, and then flatten the resulting "exon only transcripts" into a superTranscript. Aligning to this offers succint, full visualisations. We used this methodology to visualise fusion genes in the past (https://github.com/Oshlack/Clinker/), so we should just be able to do the same for Novel Splice Variants, right?

Wrong! Because so many interesting events happen within the intronic regions right? So... We need to find a way to dump the uninteresting intronic sequence, but retain the interesting.

Slinker creates a bespoke superTranscript reference based on the output of the fantastic (Stringtie2)[http://ccb.jhu.edu/software/stringtie/]. In short, we find what transcripts belong in a case sample and a control, reference and novel. Then convert this into a superTranscript. We then do some pretty, interactive plotting. Huzzah!

Slinker visualises each of the novel splicing events shown below, but naturally the transcriptome is a crazy place. So we suggest using both Slinker AND the genomic reference to figure out what is going on.

Get started here, dear reader!