Merged samples from 2 runs exist as 2 separate groups

Dear team,

I am using Qiime2 version 2020.6 currently. I merged processed samples(after DADA2) samples from 2 runs using the following command:

qiime feature-table merge
--i-tables table1.qza
--i-tables table2.qza \

qiime feature-table merge-seqs
--i-data rep-seqs1.qza
--i-data rep-seqs2.qza \

When I ran the distance matrix ordination using bray curtis and Unweighted Unifrac, I found that samples from both the run formed distinct groups. See below:


Unweighted UNIFRAC

After merging, I created a rooted-tree based on the merged table. Since we normally outsource our samples for sequencing, I am unsure if this group could be due to difference in sequencing parameter. I usually do 100000 reads/sample. I am not sure what is causing this. Please advise.



Hi @Arun04 ,
Check out this paper, specifically this figure:

looks like you have the same or similar issue (i.e., runs from different primers, or even slightly different lengths, etc).

You can check out the q2-fragment-insertion plugin to see if that fixes your issue. Otherwise scan this forum for lots of previous troubleshooting of similar issues.

Good luck!

1 Like

Hi @Nicholas_Bokulich,

Thank you for the advise. It was due to the different lengths in DADA2 trimming. Appreciate your help.



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