Q: What is the difference between USB and optical/coaxial inputs? Is one better than the other?
A: In essence they are the same -- a digital signal is a digital signal, no matter how you transport it. Having said that, there are a couple of differences:
[1] if you use USB, you can plug it into any computer. With optical or coax you need a source with an optical or coax jack. Not all computers have them, for example.
[2] At one point until not so long ago, USB technology was limited to 24 bits/48 kHz. At that time, it was much more advantageous to use optical or coax, which went up to 24/96. That technological disadvantage is no longer the case with current generation of USB chips. However, the technology has swung the other way -- many DAC manufacturers limit optical/coax thruput rates to 24 bits at 96 or 192 kHz. If you want to go higher beyond 192 kHz, for example 24-32 bit/352.8kHz-384kHz, USB may be the only way to do this. Keep in mind that your ears probably cannot tell the difference between 24/96 and 24/192.
[3] If you want DSD you may have to have USB input (of course, if your DAC does not support DSD then this is moot)
[4] if you have USB line noise from EMI (because USB carries power in addition to the audio signal) then optical/coax may get help rid of the noise (because you are not using USB)
Personally, my favorite connection is optical out, and not for any musical reason -- I just like the idea that my music traveled along a fiberoptic cable as light before ending up between my ears.
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