Reusing hints files with different isolates
Posted: Thu Nov 19, 2015 7:28 pm
Originally posted in the old forum by Jorvis on 17.01.2014 - 07:15
I'm currently working on structural annotation of 40 genomes, many of which are different isolates of the same species. In a group of 5 isolates of the same species, for example, I have RNA-Seq data for one of them and followed the protocol to use those to generate an intron hints file. Because this hints file has molecule identifiers and coordinates specific to that one organism (and the RNA-Seq integration is a long process) is there a way to build any of the information from the hints file back into the species configuration files (via e-training or optimization steps) AFTER generating the hints file so other runs of augustus using the same species params would benefit from them?
I'm currently working on structural annotation of 40 genomes, many of which are different isolates of the same species. In a group of 5 isolates of the same species, for example, I have RNA-Seq data for one of them and followed the protocol to use those to generate an intron hints file. Because this hints file has molecule identifiers and coordinates specific to that one organism (and the RNA-Seq integration is a long process) is there a way to build any of the information from the hints file back into the species configuration files (via e-training or optimization steps) AFTER generating the hints file so other runs of augustus using the same species params would benefit from them?