SOAPfuse.fusions.figure.note.for.SOAPfuse

From v1.24, SOAPfuse creates the so-called 'SOAPfuse fusion figure' for each detected fusion event.

It took Jia half a month to design and achieve it.
More work need to be done for better features of this figure.

This figure merges the old fusion figure and gene expression figure (in v1.22), clearly showing the transcript junction point, genome junction point and supporting reads alignment.

Descriptions and distribution of 12 parts are shown below with their relative locus.

|---------------------------------|
| legend and info of fusion event |  Part I
|--------------------------------------------------------------------------|
|   expression spectrum of upstream fusion partner (all exon regions)      |
|    use blue in single-sample mode;                                       |  Part II
|    use blue for control and pink for tumor in somatic mode               |
|--------------------------------------------------------------------------|
|      all exon regions of upstream fusion gene are shown                  |  Part III
|      below expreesion spectrum of upstream gene (in skyblue)             |
|--------------------------------------------------------------------------|
|      all [possible] upstream fusion transcrpts (in skyblue)              |  Part IV
|      involved by this fusion event                                       |
|--------------------------------------------------------------------------|
|      all span-reads support this fusion event                            |
|      with gray-line shows the paired-end relationship                    |
|   in single-sample mode, use blue for upstream part,                     |  Part V
|                          and orange for downstream part                  |
|   in    somatic    mode, use pink for reads from tumor,                  |
|                          and green for reads from control                |
|--------------------------------------------------------------------------|
|     bilateral detected fusion sequence of this fusion event              |  Part VI
|     blue for upstream part, and orange for downstream part               |
|--------------------------------------------------------------------------|
|  bilateral fusion segment exon-annotation based on invovled transcripts  |
|    use blue for upstream part, and orange for downstream part            |  Part VII
|    NOTE: corresponding to Part IV and IX                                 |
|--------------------------------------------------------------------------|
|      all junc-reads support this fusion event                            |
|      with gray-line shows the paired-end relationship                    |
|   in single-sample mode, use blue for upstream part,                     |  Part VIII
|                          and orange for downstream part                  |
|   in    somatic    mode, use pink for reads from tumor,                  |
|                          and green for reads from control                |
|--------------------------------------------------------------------------|
|      all [possible] downstream fusion transcrpts (in orange)             |  Part IX
|      involved by this fusion event                                       |
|--------------------------------------------------------------------------|
|      all exon regions of downstream fusion gene are shown                |  Part X
|      above expreesion spectrum of downstream gene (in orange)            |
|--------------------------------------------------------------------------|
|   expression spectrum of downstream fusion partner (all exon regions)    |
|    use blue in single-sample mode;                                       |  Part XI
|    use blue for control and pink for tumor in somatic mode               |
|--------------------------------------------------------------------------|
|      Author and Contacts        |  Part XII
|---------------------------------|

Tips:

1. In Part V and VIII, the black base shown in reads means the mismatch.
   You can determine whether it is a real SNP or just sequencing-error based on the reads number and the flanking regions.
2. Please pay attention to Part II and XII, the expression spectrum. It is important to check the different expression levels of bilateral regions around the junction point. Especially for the downsteam fusion partner. I have checked lots of classical fusion events and also some new interesting cases in my research, it is ok!
3. From this figure, you can just see the alignment of all span-reads and junc-reads. In my experience, the more even and smooth the reads-alignment distribution is, the more credible the fusion event is. I think, in the analysis of RNA-Seq data, although the number of supporting reads is important, the distribution of reads is more important. By the way, it is also important in DNA-Seq analysis.

We welcome any cogitative suggestion and discussion for better analysis.

Wenlong Jia
04-03-2013