Alpha diversity box plot

[Vara (Varalakshmi Sudagar)]

Hello,

Why in alpha diversity box plot, not all the replicates of some samples is taken into analysis to put box plot. For eg. In my data, n=3 but for some samples, alpha box plot takes only n=1. Why it is happening? Please let me know

[timanix (Timur Yergaliyev)]

Hello, welcome to the forum!
As I understood, in your feature table you have 3 replicates of certain sample, but only one is represented on the alpha diversity plots.
Did you check if number of sequences (you can visualize the table as qzv) in that samples is higher than sampling depth, chosen for ratefaction at core-metrics step? If they have lower number of sequences than sampling depth, then they will be excluded from the analysis.

[Vara (Varalakshmi Sudagar)]

Hello Timur,

Thanks. All my samples along with replicates have sequences lower than sampling depth. That'swhy don't know why in alpha box, for some samples, the replicates are not taken into account.

Thanks
Vara

[timanix (Timur Yergaliyev)]

@Vara

All my samples along with replicates have sequences lower than sampling depth

If all your samples have lower number of sequences, than diversity metrics plugin would give you an error. Could you share your feature-table.qzv file and command you are running to get core-metrics?

[Vara (Varalakshmi Sudagar)]

Hello Timur,

Thanks for your reply. One sample have features throughout the sampling depth. Is that possible if I increase my filtering read length, whether my all samples will be taken into account?

Thanks,
Vara

[timanix (Timur Yergaliyev)]

@Vara

Thanks for your reply. One sample have features throughout the sampling depth. Is that possible if I increase my filtering read length, whether my all samples will be taken into account?

Hello!
I am afraid, I can not understand clearly your last question.
But if you want to get more samples for alpha diversity plots, you should try to lower sampling depth value in your core-metrics command.