# Analyzing two different runs separately **URL:** \ **Category:** Theory behind mothur\ **Created:** [December 9, 2025, 7:08pm UTC](https://forum.mothur.org/t/analyzing-two-different-runs-separately/22391 "2025-12-09T19:08:12Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![mainly.microbe](https://avatars.discourse-cdn.com/v4/letter/m/77aa72/32.png) [@mainly.microbe](https://forum.mothur.org/u/mainly.microbe)\ **Post date:** [December 9, 2025, 7:08pm UTC](https://forum.mothur.org/t/analyzing-two-different-runs-separately/22391/1 "2025-12-09T19:08:12Z")
Hi all, I am analyzing two different sequencing runs that do not align to the same start/end when aligned to the silva database. So running them together using the mothur SOP is not working. I wanted to merge the OTU tables but that doesn’t seem to be feasable either. Ive decided to just switch gears and analyze them separately and compare. If I do this, does that mean I cant run beta diversity metrics or pcoa etc because theyre seperate runs? Or is there a way to compare them in mothur? Im primarily interested in understanding the change in diversity between the two batches. ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [December 11, 2025, 3:00pm UTC](https://forum.mothur.org/t/analyzing-two-different-runs-separately/22391/2 "2025-12-11T15:00:48Z")
My suggestion in these cases it to treat them as two separate datasets. Draw your inferences from each and then determine whether those inferences agree. Pat ---
**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\ **Post date:** [December 21, 2025, 3:00pm UTC](https://forum.mothur.org/t/analyzing-two-different-runs-separately/22391/3 "2025-12-21T15:00:50Z")
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