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we are working on Standalone USB to USB file transfer device
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Why? What is the point? There would be no market for it.
I can take a piece of wire (ethernet cable) and make an ethernet-to-ethernet file transfer device much easier :)
But seriously, what are you really trying to do?
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plan is to make a usb controller in DE0-nano dev kit as well as the microcontroller inside it. Do we need to purchase IP Cores regarding the USB Controller? or can we design it by ourselves?
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You don't even start there. You buy a microcontroller with two USB interfaces on it. Both of them need to be device interfaces if you expect to be able to have two PCs (hosts) view the micro as a USB device.
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any pointers to read about? and about the microcontroller inside the fpga, is the nios II processor already included in the Quartus II? Thank you.
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You are going about it completely wrong. The new ARM Cortex microcontrollers come with a library called CMSIS that creates a uniform layer for USB interfaces on Cortex microcontrollers from all vendors. If you really want to create something that is file-system to file-system, then you have a need for
software, not FPGA logic.
Perhaps you could explain the application a little more clearly? That way we can see if there really is a need for an FPGA.
Cheers,
Dave