Beta diversity raw data output

Dear QIIME developers!

I have performed some diversity analyses on my fungal data using the qiime diversity core-metrics and qiime diversity beta-group-significance. To look more into the beta diversity data, I downloaded the raw data from the qzv file, and also exported data from the Bray-Curtis matrix. Furthermore, I did the same thing with the corresponding data in the Moving Pictures Tutorial. The data look somewhat different, and it would be great if you could help me with some input on this:

  • In the last column in the raw data (Distance), almost all of my values are “1” (actually 47317 of 68746)
    Additionally, the rest of the values have a maximum of 4 decimals, and always end with 5 or 0 (0.0125, 0.025, 0.0375, 0.05 and so on). The corresponding data from the MPT looks more “random” (e.g. 0.810516772 and 0.224841342), and only 70 of 823 is the value “1”. Do you know why? Could it have something to do with the rarefaction?

  • Looking at the distance matrix, the same phenomenon seems to occur: Lots of 1-values, and the rest have a maximum of 4 decimals, and always end with 5 or 0. Again, the distance matrix from MPT has more decimals, and looks more “random”.

Grateful for some information or suggestions on this!

Whole commands:

qiime diversity core-metrics \
  --i-table table.qza \
  --p-sampling-depth 80 \
  --m-metadata-file metadata.txt \
  --output-dir Diversity_metrics

qiime diversity beta-group-significance \
  --i-distance-matrix Diversity_metrics/bray_curtis_distance_matrix.qza \
  --m-metadata-file metadata.txt \
  --m-metadata-column SampleType \
  --o-visualization bray_curtis_sample_type.qzv \
  --p-pairwise

this is an extremely low sampling depth and almost certainly the issue. E.g., at that sampling depth many of your samples may have no shared features, which would result in a distance of 1.0 with Jaccard and UniFrac.

use a higher sampling depth, even if it means losing some of your samples.

good luck!

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