Lane files have been often processed outside emBASE and demulitplexed files are stored somewhere. Features like lane file deletion, MAGE-TAB export require that demulitplexed files are made available to emBASE. You can now easily move your demulitplexed files back to the right place automatically with the newly released AddLibraryFilesToNGSRepository command line tool. Read more here

Or simply call java -jar /g/funcgen/gbcs-tools/embase-cmdline/AddLibraryFilesToNGSRepository.jar -h