Loading sequence files
Lucy2 accepts most genome sequences as a sequence file (.seq); however there are others that may be acceptable. Simply left click on Open or select Files > Open files from the pull down menu. In this tutorial, we will use the Atie.seq downloadable from our website. Be sure to save the file to your computer as a .seq file, not as a .txt file. Also download all files associated with it available on our website. Select the file and choose open. A pop up box will display:
This dialogue box searches for parameters and quality values already set from the original Lucy. Quality files have the extension .qul, in addition, there are two parameter files named PUC19 and PUC19splice that will also be used during this tutorial. Choose Yes.
The sequence is now loaded into the program. Use the scroll down menus to view the sequences and numbering.
Computing Quality Value
Lucy2 allows the parameters to be specified before calculations. Please see the paper, DNA sequence quality trimming and vector removal by Hui-Hsien Chou and Michael H. Holmes for more information about setting parameters. The following four screens are the windows available to set parameters;
To compute quality values based on the programs pre-set parameters, left click the Run or choose File > Run from the pull down menu. The following screen will appear as Lucy calculates quality values: