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Add mermaid schematics
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lonsbio committed Feb 16, 2022
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![Toblerone](img/logo.png)
# Toblerone

Toblerone is a method for detecting internal exon (not first or last) deletions in RNA-seq data. It is currently in development, extending the methods described here for acute lymphoblastic leukemia (ALL) focal deletions in IKAROS family zinc finger 1 (IKZF1) : https://github.com/Oshlack/ALL-RNAseq-utility-paper
Toblerone is a method for detecting exon deltions in RNA-seq data. You'll notice in the logo that an e(xon) is missing!

It is currently in development, extending the methods described here for acute lymphoblastic leukemia (ALL) focal deletions in IKAROS family zinc finger 1 (IKZF1) : https://github.com/Oshlack/ALL-RNAseq-utility-paper. Toblerone looks for internal exon (not first or last) deletions.

Toblerone consists of two key concepts: a specialised transcriptome and a modified pseudoalignment algorithm

A desktop app is also available for single sample analysis.



## Pseudoaligner

The psuedaligner core is currently called `tinyt` and can be run in standalone mode form the command line, or is inclued in the Toblerone app (see below).
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For a candidate gene, e.g. IKZF1, we take the the canonical transcript and generate a specialized transcriptome reference that consists of the original transcript plus deletion transcripts. Deletion transcripts consist of combinations of continuous exon deletion, excluding edge exons (first and last) exons. For N exons, (N-1 choose 2) additional deletion transcripts created.


```mermaid
graph TD;
A[\input gene defintion/]-->B;
B[generate deletion definitions]-->D;
C[\input transcriptome/]-->D[create deletion transcripts];
D-->E[index];
```

##### Generate transcripts

For the gene(s) of interest, a canonical transcript should be provided which is the full length in order for the maximum number of exon deletions to be captured. Currently only `BED12` file format is accepted.
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Reads can now be mapped and the counts, proportions and scaled proportions of deletions in a sample can now be calculated:


```mermaid
graph TD;
A[\toblerone_transcriptome/]-->C;
B[\input RNA-seq reads/]-->C[tinyt map];
C-->E[Deletion summary csv];
```



```
tinyt map -i toblerone_transcriptome.tidx <reads>
```
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