choosing of sampling depth

[Gaaviya (Gaaviya R S)]

1. 

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1st image - highest sampling depth - 11885
2nd image - lowest sampling depth - 3202

according to the image given , can u tell the exact sampling depth to be done?? and explain it why the specific value has taken?

[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…

[Gaaviya (Gaaviya R S)]

Thank you sir/mam

qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--p-sampling-depth 1103
--m-metadata-file sample-metadata.tsv
--output-dir core-metrics-results

for this code, instead of 1103 , can u give the round off sampling depth value for my samples as i gave you the pictures above for reference?

[gregcaporaso]

@Gaaviya, Colin is suggesting that 3202 might be a reasonable choice, but I highly recommend reading the post that he shared with you. There is not a single right answer to this question: it depends on your data.

[Gaaviya (Gaaviya R S)]

can u tell the max depth according to the feature table i had given??

[colinbrislawn (Colin J Brislawn)]

Can you share the full command you are running?

[Gaaviya (Gaaviya R S)]

qiime diversity alpha-rarefaction
--i-table table.qza
--i-phylogeny rooted-tree.qza
--p-max-depth 4000
--m-metadata-file sample-metadata.tsv
--o-visualization alpha-rarefaction.qzv

This 4000 is an example dataset in qiime2 tutorial

Tell the Max Depth for my dataset as i already shared u all my dataset sample from dada table output file

[colinbrislawn (Colin J Brislawn)]

Thank you for sharing your full command.

When I run this command, I set max-depth to be near my sample with the most reads. Based on your example, this would be 11k or 12k.

Tell the Max Depth for my dataset

This is not my decision because this is not my project.
This is your project, and your work is your work.

Let me know if you have more questions about Qiime2!