Editing the human trackDb.ra file
Human assemblies do not display chain/net tracks in the same way that other assemblies do. In most assemblies, the chain/net tracks are listed individually in the Browser's track listings. In human assemblies, there are three composite tracks called "Primate Chain/Net", "Placental Chain/Net" and "Vertebrate Chain/Net". In order to add new chain/net tracks to these composite tracks and so they don't appear individually, you must edit the human trackDb.ra file.
Location of the file
The path to trackDb is /kent/src/hg/makeDb/trackDb, but for simplicity's sake, when referring to trackDb, I will just say /trackDb.
As with trackDb.chainNet.ra, there are two versions of trackDb.ra. One is located in the /trackDb/[organism] directory and one is located in the /trackDb/[organism]/$db directory. For example, the latest human assembly has a file in /trackDb/human and a file in /trackDb/human/hg19. The file in /trackDb/human/hg19 applies only to hg19 whereas the file in /trackDb/human applies to any previous human assembly, to hg19 and also any future human assembly. Unlike with trackDb.chainNet.ra, you want to make sure that you edit the version of trackDb.ra at the database-level directory.
Structure of the file
The trackDb.ra is long and complex, but there are only three sections to be concerned with:
- primateChainNet
- placentalChainNet
- vertebrateChainNet
The instructions for editing the file differ depending on whether you are adding an assembly that is replacing an older assembly, such as gorGor3 replacing gorGor1, or adding a brand new assembly that does not yet exist in trackDb.ra.
Adding an assembly that replaces an old assembly
Adding an assembly to replace an old one is not very difficult.
