Importing data for PCoA analysis (alpha-, beta-diversity)

Hello there,

I have a question for importing data for further analysis
I have several datasets analyzed by qiime2 separately since I have collected data based on yearly and areas.

For analysis it’s beta-diversity to compare samples yearly, and based on area, I want to import old data and compare.

Which data should I import from previous analysis for using ‘qiime-diversity’??, and How?

I have several data files for each analysis.

Or should I analyze all together again for doing this?

Best,
Jun

Hi @junkim83,

This is a slightly tricky question. If the data was analyzed before 2018.4 (I think) you will need to re-process it, since the artifact format changed slightly at either 2018.4 or 2018.7 and 2018.11 is not forward compatible with the previous version.

If you used similar processing steps (same region, same algorithm, same parameters), it should be okay to just combine your feature table, repset and taxonomy. Otherwise, I would deblur all your sequences using the same parameters.
Then, you want to combine the databases using qiime feature-table combine (double check the feature table plugin). You should also find rep-set combining in the feature table plug-in. Then, rebuild your tree and go forward.

If you did not use the same primers, cluster your data closed reference and then pass that into the diversity analyses.

Best,
Justine

2 Likes

Hi @jwdebelius,

Thanks for your reply.

OK… I need to reprocess my data since I used different versions for each dataset.
It will take crazy days…

Thanks anyway! It was a great help.

Best,
Jun

1 Like

Hi @junkim83,

My suggestion would be to check the versions of the core programs you used (like if you used dada2 v0.1.1 in qiime2-2019.1 and qiime2-2019.4, I would worry less). But, in that case, perhaps deblurring makes sense? Or look at some of the recommendations around meta anlaysis.

Best,
Justine

1 Like

Hello @jwdebelius,

I’m trying to alpha, beta diversity from separated generated qiime2 artifacts as you suggested.
For the diversity analysis, I need table.qza and rooted-tree.qza files. Also, for generate rooted-tree.qza file, I need rep-seqs.qza file.

As you suggested I know the how merge the table.qza file now but I can I merge the several rep-seqs files previously generated?

Thanks for your help Always!

Best,
Jun

1 Like

I found How to do this in previous posts.

Thanks Junstine!!

Jun

2 Likes

Hi @junkim83,

I’m glad you solved it! Let us know if you have any more questions, but sometimes figuring it out on your own is better because they you’ll remember.

Best,
Justine