How to compute several alpha-diversity rarefaction plots

hi! sorry I am trying to compute several alpha-diversity curves through qiime diversity alpha-rarefaction plugin. Similar to qiime1, I’m trying to pass through command line. I’ve tried in a text file (similar to qiime1 alpha_diversity:metrics X,X), also trying as --p-metrics X,X; --p-metrics X|X… but it does not work!

1 Like

Hi @matoro,
Thanks for posting! I am a little unclear on your question — are you trying to compute alpha rarefaction plots with multiple metrics at once? Or are you trying to use a QIIME1 text file as input? I assume the former, based on the title.

To compute multiple metrics, you need to pass the metrics parameter multiple times if you want to use metrics other than the default. E.g., --p-metrics X --p-metrics Y --p-metrics Z

Please let me know if that solves your question!

3 Likes

Yes!!! it solves! I think it was the only way I didn’t try.

Thank you! (I’m on the way to go from Qiime1 to Qiime2, step by step).

1 Like

Thanks for confirming! Happy to help.

Welcome to the QIIME2 family! :family_man_woman_girl_boy:

If you haven’t already, check out the docs and tutorials at https://docs.qiime2.org/ to help you make the switch. In-depth information on the available plugins/actions is here (e.g., I answered your question by checking out this page) and the tutorials have lots of useful information to aid in the transition.

Happy QIIMEing! :beach_umbrella::sunglasses::sun_with_face:

1 Like

Thanks! I’m performing right now tutorials! thank you!

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.