Hello, I have started using Artemis for the first time as a way to overlay next-gen sequencing data onto annotated bacterial genomes. It has the capability of doing everything that I need it to do, but I am having trouble with my own custom user plots. It is probably something that I am doing wrong, but I just can't seem to figure it out on my own! Any clues would be greatly appreciated.
I am using Artemis 10 standard release, with Java 6 update 10, on Window XP professional SP 2, fully updated. Artemis appears to be working well. To confirm this I downloaded the supplementary data from http://www.biomedcentral.com/1471-2164/9/364, and I was successfully able to open and view the custom user plots on the provided gbk file. However, I am unable get my own custom user plots to be successfully opened in Artemis. I am creating these on a separate machine (running RHEL 5), copying the space delimited format seen in the above data set. I do not get any error messages, the plots just don't display. I think this might be an EOL/encoding issue because if I attempt to modify the user plots downloaded above (using either word, notepad, wordpad, or excel but saving as "text"), then these also fail to load. I have tried without success: * renaming the file * unix2dos before binary transfer to the windows box. * unix2dos before ascii transfer to the windows box. * opening the file using windows/word/notepad/excel and pasting/saving to a new text file. According to the "file" program on unix, the downloaded data and the post unix2dos custom data have the same encoding, so I don't really know where to go from here. I have been through Google, and through the archives for this mailing list without success - so either I am doing something completely moronic, or no one else in the world is having this issue! Any help/suggestions/flames (do people still say "flame"? =) ) would be greatly appreciated. I need to get this working on a Windows system, because that's what the end users of this data will be using. Cheers, Nicole.
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