Hello @Dawud922 ,
Welcome back to the forums.
You have discovered a fundamental trade-off between keeping more samples and keeping more depth. Chris wrote up a great discussion of this trade-off, if you want to take a look:
Hi again @ptalebic !
These are good questions, and have been discussed at length here on the forum. I've done my best to answer them again here, but you'll really want to dig into the resources at the end of this response.
Your sampling depth is quite good, so you have more wiggle room than most studies. You're mostly right that the goal here is to find a balance between "the most sequences" and "the most samples". Considering how metadata categories are impacted is critical.
For example:
Yo…
So, "what does your study need?"
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