Has anyone ever had to load additional read info AFTER the database and the assembly have been created. I managed to convert an .ace file (from another assembler, not phrap) to an .aux database, and Gap4 loads and displays it fine. However, none of the template or vector information made it in. Now I've updated the .exp files with all the right tags but can't figure out how to make Gap4 re-process them.
The best bet is to do an extract readings in directed assembly format, munge the resulting exp files, and then create a new database and use directed assembly to import them back again.
Alternatively (and how we work at the Sanger Institute) use the caftools package. gap2caf, munge caf and then caf2gap works wonders.
If you want to go direct gap4 does have scripting interfaces for directly editing data in situ though. See http://staden.sourceforge.net/scripting_manual/scripting_toc.html for details.
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