I keep having trouble with a win computer at work. It says my usb stick is infected, and will not read my data. My Ubuntu computer reads them, no trouble, and clamscan finds no virus.

I think the virus is coming from the Win computer, which has AVG as antivirus program. I need to use this computer now and again to print things, that's all I do with it. Our printer is a Toshiba eStudio 243 multifunction machine, which will not work with Linux.

I have reformatted my usbstick, replaced the files on it from my back up, run clamscan on it. I insert it, the win computer can read it. The next time I do this, I get AVG saying everything is infected, and the win computer won't read my stick. It's a bit of a problem when I want to print something in a hurry.

As I did not use my stick on any other win computer, I think the problem starts there.

So I want to run clamscan from a Ubuntu boot stick that I have, put it in the win computer, boot from usb then run clamscan, find what AVG is missing and remove it.

Can this be done? If so, please tell me what I need to put on the usb stick.

Ok I think were your going with this. Anti-virus is falsely reporting an infection on your usb drive and you want to check windows for malware/viruses on the windows machine.
You need a portable bootable Linux install on a USB flash drive (not live distribution) and in install clamav from the package manager. You can change the boot order to USB,CDrom,hard disk. You can scan it from the portable Linux. Your Company policy may prohibit you from doing this. Anti virus is not prefect and may reject revolvable media for all kinds of reasons. Disabling AV on revolvable media might be OK for you but can open windows attacks.