choosing of sampling depth

[colinbrislawn (Colin J Brislawn)]

Hello Gaaviya,

Welcome to the forums!

This is a hard question because there is no perfect answer. This is a balance between keeping more samples and keeping more reads from each sample. The good news is that 3.2k or more reads per sample is pretty good, and I've seen papers published with fewer reads.

Chris has an excellent explanation about how to use the Sampling Depth tool to see which samples from your various cohorts will be lost at a given depth threshold so you can make an informed decision for your data set.

Sampling depth - Is my sampling depth ideal

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…