I am relatively new to qiime, so I’m sorry if this question is too basic I was wondering if there is a plugin that gives me a list of OTUs per sample type. For example, I have three sets of data for patients with C.diff , patients showing C.diff symptoms but with no C.diff, and healthy volunteers. What I am trying to do is getting a list of OTUs per cohort so I can run them through a Venn diagram and see how many of these OTUs are unique, dually shared, and present among the three cohorts.
Thanks a lot! (
You may want to try filtering your table using
qiime feature-table filter-samples and specifying the
--p-where parameter. That will give you three separate tables of features with those that are only present in t he table. (If not, you can apply a second
filter-features and remove anything below 0 counts… or whatever your threshhold of choice is.) I’m not sure if QIIME has the capacity to do the venn diagram (you can always check the core plugins for their functions). But, the artifact interface serves me well for jumping back and forth with python, and a lot of people like qiime2R.
Yes! That did the trick! I couldn’t find any Venn diagram plugins but I got the list anyway, so thanks a lot!
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.