SOAPfuse Wiki

a tool for identifying fusion transcripts from paired-end RNA-Seq data

Brought to you by: jwl890427

Output Files

All final results are stored in this directory:

$ cd /out_directory/final_fusion_genes/sample-ID_or_patient-ID/

Note:

v1.25

here

v1.22

sample-ID_or_patient-ID.final.Fusion.specific.for.genes

This text file contains the predicted fusion events specific for genes. The format of this file is:

Column_NO.     Descriptions
   1           up stream fusion gene (5' partner)
   2           chromosome of up stream fusion partner
   3           strand of up stream fusion partner
   4           genome junction position of up stream fusion partner
   5           location of up stream fusion partner's junction point
   6           down stream fusion gene (3' partner)
   7           chromosome of down stream fusion partner
   8           strand of down stream fusion partner
   9           genome junction position of down stream fusion partner
  10           location of down stream fusion partner's junction point
  11           number of span-reads (details in sample-ID.final.Span_reads)
  12           number of junc-reads (details in sample-ID.final.Junc_reads)
  13           classification of fusions
  14           whether down stream fusion partner is frame-shift or in-frame-shift

sample-ID_or_patient-ID.final.Fusion.specific.for.trans

As we know, each gene has its specific transcript isoform(s), and lots of genes have multiple isoforms. From v1.24 version, SOAPfuse detects fusion transcripts for each transcript isoform. For example, one fusion partner, Gene-A, its junction point may be covered by several transcript isoforms, such as A-001 and A-201. And its fusion partner, Gene-B, is also in the same situation. So, for one fusion gene pair (A-B), you could find several corresponding fusion transcripts, each one consists of one isoform of Gene-A and one isoform of Gene-B.
This text file contains the predicted fusion events specific for transcript isoforms. The format of this file is:

Column_NO.     Descriptions
   1           up stream gene (5' partner)
   2           up stream transcript isoform
   3           chromosome of up stream fusion partner
   4           strand of up stream fusion partner
   5           transcript junction position of up stream fusion partner
   6           genome junction position of up stream fusion partner
   7           location of up stream fusion partner's junction point
   8           down stream gene (3' partner)
   9           down stream transcript isoform
  10           chromosome of down stream fusion partner
  11           strand of down stream fusion partner
  12           transcript junction position of down stream fusion partner
  13           genome junction position of down stream fusion partner
  14           location of down stream fusion partner's junction point
  15           number of span-reads (details in sample-ID.final.Span_reads)
  16           number of junc-reads (details in sample-ID.final.Junc_reads)
  17           classification of fusions
  18           whether down fusion partner is frame-shift or in-frame-shift
  19           type of up stream fusion isoforms
  20           type of down stream fusion isoforms
  21           the area where up stream juction point locates
  22           the area where down stream juction point locates
  23           whether the up stream isoform has the start codon (in database)
  24           whether the up stream isoform has the stop codon (in database)
  25           whether the down stream isoform has the start codon (in database)
  26           whether the down stream isoform has the stop codon (in database)
  27           whether the fusion structure has the stop codon
  28           the information of fusion peptide chain

sample-ID_or_patient-ID.final.Span_reads

This text file contains the detailed information of span-reads.

sample-ID_or_patient-ID.final.Junc_reads

This text file contains the detailed information of junc-reads.

initial_fusions/

This directory contains the initial fusion events before filtering.

abandon_fusions/

This directory contains the fusion events abandoned by different filterings.

analysis/

This directory contains the further analysis of final fusion events.

In For_RT-PCR_validation directory
a. sample-ID_or_patient-ID.trans.fused.seq.for.RT-PCR
    This text file contains the bilateral segment around junction point of each fusion transcript. It
    is corresponding to the sample-ID_or_patient-ID.final.Fusion.specific.for.trans file. The up
    stream segment is separated with the down stream segment with vertical line '|'. The segments are
    very useful for users to construct the primers for their further RT-PCR validation experiments
    of concerned fusion events. It has been proved useful and correct by several fusion research
    projects in BGI.

    Format:
```
    Column_NO.     Descriptions
       1           fusion event specific for genes
       2           fusion event specific for transcript isoforms
       3           bilateral fusion segments separated by '|'
```
In For_peptides_analysis directory
a. sample-ID_or_patient-ID.trans.fusion.peptide.chain
    This text file contains the predicted fusion peptide chains corresponding to all fusion
    transcripts that are annotated as 'inframe-shift' in sample-ID_or_patient-ID.final.
    Fusion.specific.for.trans file. You can use the peptide chain string to study the domain
    regions in iprscan website.

    Format:
```
   Column_NO.     Descriptions
       1           fusion event specific for transcript isoforms
       2           whole fusion segment
       3           fusion peptide chain string
```
In figures directory

a. fusions_expression sub-directory
    This sub-directory contains the so-called 'SOAPfuse fusion figure' (svg/png) of each fusion
    events. 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. It
    is useful for users to select the interesting fusion events.
    Set config parameter 'PA_s09_draw_fusion_expression_svg' as 'yes', and enjoy this figure.
    click here for more information about SOAPfuse fusion figure.
    click here to see one instance of TMPRSS2-ERG from one prostate cancer sample.
    click here to see one instance of somatic KIF5B-RET from one lung cancer patient.
    Note:
    'SOAPfuse fusion figure' is totally designed and achieved by Wenlong Jia in BGI. We will
    apply for a patent for this figure.

b. landscape_of_fusions sub-directory
    This sub-directory contains the so-called 'SOAPfuse 3D landscape figure of fusion' (svg/png)
    of concerned sample/patient. This figure displays all detected fusion events in 3D pillar array.
    Fusion events are shown with SOAPfuse-score, Fusion-type, inframe-shift-or-not,
    fused-at-exon-edge-or-not and whether-is-somatic (in somatic running mode). It is also useful
    for users to select the interesting fusion events.
    click here for more information about SOAPfuse 3D landscape figure of fusion.
    click here to see one instance of one prostate cancer sample harboring TMPRSS2-ERG.
    click here to see one instance of one lung cancer patient harboring somatic KIF5B-RET.
    Note:
    'SOAPfuse 3D landscape figure of fusion' is also totally designed and achieved by Wenlong Jia
    in BGI. Using 3D scale to display bioinformatic value distribution is common, but to our knowledge,
    this is the first time that it is used in the fusion gene research.