Compare different sequencing data with different sequencing depth

[doudou2047 (孟琼)]

Hi, Gooday,
Thank you. I did an interesting test.
I sequenced same genomic DNA (18 in total) by different sequencing center, with different sequencing depth.
I would like to compare the two piece of data. So, I combine the 36 sequence data (18 with higher depth, 18 with shallow depth).

I used the DADA2, with the same parameter.

The alpha-rarefraction plot like that:

The taxa bar plot like that:

The paired-end-demux.qzv view like that:

Could you please help me with the questions?

1. The alpha-rarefraction plot, the x-axis (0-2200) means? What's the scale mean?
2. The taxa bar plot lost the information of the shallow sequence data, however, when I only check the shallow sequenced data, the performance is not that bad. Do you have any suggestions?
   The 18 samples with shallow sequencing depth, we get results, like that:
   
   
   
   
   

[colinbrislawn (Colin J Brislawn)]

Good afternoon!

Those plots look good. I'm glad you got all the way through alpha rarefactions plots and bar plots.

Your questions are also good, and many of the answers are in the tutorials. For example, when you ask,

@doudou2047

• The alpha-rarefraction plot, the x-axis (0-2200) means? What’s the scale mean?

That's a good question that's answered in Moving Pictures tutorial. Bonus, there's also a translation of the Moving Pictures tutorial!

Take a look at how the Moving Pictures tutorial interprets those results, then let me know how they compare to your data.

Then we can help answer any more questions you have.

Colin