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I guess maybe I haven't figure out your project, since its the first time I'm working with qsys and with sdram.
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You'll need to read through the Quartus handbook :)
This tutorial walks through some of the details:
http://www.alterawiki.com/wiki/using_the_usb-blaster_as_an_sopc/qsys_avalon-mm_master_tutorial --- Quote Start ---
What I am trying to figure out is, how do I work with the controller that is given from ALTERA IP catalog.
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Altera supplies all of their IP with a bus interface they call "Avalon". The interface supports reads, writes, and bursts, etc. Altera's Qsys tool allows you to connect multiple Avalon devices together, to define an address map, and then generate the interconnect (address decoding, data demultiplexing, and arbitration code).
If you want to interface to the SDRAM directly, then you could create an Avalon-MM master interface state machine.
Why don't you explain what you are actually trying to do. There may be Avalon components that can be used.
Cheers.
Dave