Question about read table to use for q2-SCNIC

(Jonathan Gaiero) #1

Hi there,

Just a couple (hopefully) quick questions.

A. Rarefying is commonly used in QIIME analyses. I’m wondering if this rarefied table can (or should) be used in q2-SCNIC?

B. Are we to use the unfiltered table in the make-modules-on-correlations command or the ‘sparcc-filtered’ table that we output after step 1 (and the one we calculated correlations from)?

In step 3 of the tutorial, the command is as follows

qiime SCNIC make-modules-on-correlations
–i-correlation-table fake_correls.qza
–i-feature-table fake_data.qza
–p-min-r .35
–o-collapsed-table fake_data.collapsed.qza
–o-correlation-network fake_net.modules.qza
–o-module-membership fake_membership.qza

Thanks a lot for your help!