meta-analysis and q2-fragments

General Discussion
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1

Hi everyone
I am working in meta-analysis to find the geographical and phylogenetic variation of gut flora. For this I took 6 study data with different primer set, I had preformed the DADA2, Taxonomy and core diversity separately, and also i have completed the q2-fragment insertion and filter the table with insertion-tree. From here I didn’t known what to do. Either i have do go with separate taxonomy file or with q2-fragment insertion.

If i want to proceed with q2-fragment for diversity, taxonomy and core-diversity, what i have do .
Please suggest me with workflow
Thank you for your valuable

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2

What are your biological questions?

Sounds like they involves geography :earth_africa: and phylogeny :palm_tree:

Once I know more about your questions, maybe I can suggest an analysis to get answers.

Colin

3

Hi Colinbrislawn
I have taken five species of nematode guts micro flora study from NCBI-SRA (50 bioprojects) belongs to from different part of the world. I want to know the variation/uniqueness and commonly occurring species of microbial flora between and within the nematode species. so that i can continue my sample collections based on the results.

4

Hi
I want to merge the q2-fragment insertion tree from to different studies. I have search the qiime2 libraries i couldn’t find it. so please help me in this.
Thank you

6

Hello again,

This sounds like a great study! :earth_africa: :earth_americas: :earth_asia: :microbe:

I would recommend using these two plugins to see how diversity changes based on location, study site, lattitude and such.
https://docs.qiime2.org/2019.10/plugins/available/diversity/core-metrics-phylogenetic/
https://docs.qiime2.org/2019.10/plugins/available/diversity/beta-group-significance/

Once you have groups you want to compare, you can use this plugin to see which microbes are driving this change:
https://library.qiime2.org/plugins/q2-aldex2/

Let me know what you find!

All the available plugins :point_right: Available plugins — QIIME 2 2019.10.0 documentation
The fragment-insertion plugin: fragment-insertion — QIIME 2 2019.10.0 documentation

Colin

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8

Hi Colin
Thanks for your useful suggestions
Now i couldn’t find the command to merge insertion tree for different study. Will you please suggestion any other method.

Also i have merge the table and rep-seqs of different study and try to run the qiime fragment insertion sepp, but it takes more than 32 hrs and still running, my hpc config is 96 gb RAM and 240 core, is their any short cut to run this command.
Thank you

9

merge the tables/seqs for the studies before running fragment-insertion.

this is indeed a very time- and memory-intensive step. Especially if you are performing a large meta-analysis, I am not surprised at the amount of time it is taking.

1 Like
10

Hi @kulandai1

How long did your fragment insertion take to finish?

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@Huda_Ghori It took more than 48 hrs.