4. How to make a .brk file

A .brk file is the file format that created to locate the fused gene split point coordinate(s). In addition to the coordinate information, chromosome or scaffold sequence ID and fused gene ID are also included. Below is an example of the .brk format.

Open .brk file in a text editor:

_images/brk.png

Open .brk file in MS excel:

_images/brk2.png

By default, the mid point of putative fused gene models are suggested as breaking point to split putative fused genes, but the breaking point for the gene models with 3 or more fused genes need to be manually curated. To determine the breaking points, gene models need to be visualized in a genome browser, such as Jbrowse.

4.1. Prerequisites

  • Complete step 1: detect fused genes
  • .brk file: breaking_point.brk
  • Text editor, MS Excel or other alternatives
  • Load your MAKER genome annotation into a genome browser, such as Jbrowse

4.2. Setup Jbrowse instance

To install Jbrowse and setup Jbrowse instance, please refer to Jbrowse_tutorial.

4.3. Fused gene model - scenario 1

_images/fused_scenario_1.png

4.4. Fused gene model - scenario 2

_images/fused_scenario_2.png

4.5. Fused gene model - scenario 3

_images/fused_scenario_3.png

4.6. Fused gene model - scenario 4

_images/fused_scenario_4.png

4.7. Edit .brk file in text editor or MS excel

The most convenient way to edit the .brk file is in the MS excel or other tab-delimited editor GUI alternatives.