Linux on a pendrive

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Thought i would throw this out there to the those that have far more experience than i in this matter. I have a need to create a bootable USB pendrive, easy enough, thanks to the LiveUSB-Creator tool provided on the fedoraproject site. But what i need is a desktop linux (KDE preferred) with some additional RPMs and Applications on it (Scientific based apps like PyMol) on a pendrive. I have created the pendrive with quite a bit of space for persistent storage, but wanted some opinions on the best way to move forward.

Thanks in advance for any direction
Michael Weiner
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