Fundamental difference with certain Avalon Signals

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http://www.altera.com/literature/manual/mnl_avalon_spec.pdf (http://www.altera.com/literature/manual/mnl_avalon_spec.pdf)

But to answer your question ... Chipselect is enabled any time that the avalon bus is actively talking to your component (or from your component if it's a master). Begintransfer is only active at the beginning of a transfer. You would likely only use this if your custom user logic allowed burst transfers which it probably does not. Also, I don't even know if the instruction and data master ports on the NIOS processor support this signal. However, the DMA module does.