When I am transferring into the second container do I want to avoid getting any of the yeast cake? Or do I want some of the yeast/hops for secondary fermentation? Any thouts would be helpful. I am working on an Arrogant bastard clone.
"Secondary fermenter" is a misnomer in beer brewing. You should wait until primary fermentation has finished. In other words wait until you have stable gravity readings over three days, then transfer. Added: Do not transfer the yeast cake, but do not worry if you get a little in the secondary.
A more accurate description would be Bright Tank or Clearing Tank. This is just a step to let the sediment in the beer to settle out.
You can also skip this step entirely. Just leave the beer in primary until you reach your final gravity then leave it alone for another week or two then bottle.
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