How to merge the tables?

[codea (Christian)]

Continuing the discussion from Combining data from different sequencing centers and primers:

@Mehrbod_Estaki

a) Treat the 2 tables separately all the way until you assign taxonomy to them, then merge the tables.

Touching on this point, what are you using to merge the tables? Thanks in advance.

[thermokarst]

Hey there @codea!

@codea

Touching on this point, what are you using to merge the tables?

Take a peek at feature-table merge - that should get you started. As well, the FMT Tutorial has an example of merging runs, which involves merging a few different semantic types together.

Keep on QIIMEin'

[codea (Christian)]

@thermokarst

Take a peek at feature-table merge

Great thank you,
I've taken up this plugin and entered the following so i can hope to merge and compare my 2 regions:

(qiime2-2018.8) codea@lsp-bioinfo03:~/Data/mergev1v3v3v4$
*qiime feature-table merge *
*--i-tables dada2-tablev1v3.qza *
*--i-tables dada2-tablev3v4.qza *
--o-merged-table dada2-table_merged.qza

I got this error:

Plugin error from feature-table: Same samples are present in some of the provided tables: elandapoint, cootharaba, marycairncross, twinwaters, palmercoolumresort, usc-BPHLF

Debug info has been saved to /tmp/qiime2-q2cli-err-568yazw0.log

The 2 dada2 table inputs do have the same names as they are the same samples but being read using 2 different 16S regions.
I've seen a parallel post to this problem, where you quoted to use the following parameter:

--p-overlap-method [sum|error_on_overlapping_feature|error_on_overlapping_sample]
** Method for handling overlapping ids.**
** [default: error_on_overlapping_sample]**

Unfortunately i get the following error:

(qiime2-2018.8) codea@lsp-bioinfo03:~/Data/mergev1v3v3v4$ qiime feature-table merge
--i-tables dada2-tablev1v3.qza
--i-tables dada2-tablev3v4.qza
--o-merged-table dada2-table_merged.qza
--p-overlap-method [sum|error_on_overlapping_feature|error_on_overlapping_sample]

error_on_overlapping_feature: command not found
error_on_overlapping_sample]: command not found
Usage: qiime feature-table merge [OPTIONS]

Error: Invalid value for "--p-overlap-method": invalid choice: [sum. (choose from error_on_overlapping_sample, sum, error_on_overlapping_feature)
(qiime2-2018.8) codea@lsp-bioinfo03:~/Data/mergev1v3v3v4$ Method for handling overlapping ids.
Method: command not found
(qiime2-2018.8) codea@lsp-bioinfo03:~/Data/mergev1v3v3v4$ [default: error_on_overlapping_sample]
[default:: command not found

I can see im doing something wrong, i apologise in advance if this needs to be posted elsewhere.

Thanks again.

[Mehrbod_Estaki]

Hi @codea,

The --overlap-methodparameter requires that you choose one of the three methods listed in the square brackets. For example
--p-overlap-method sum

That being sad, is your ultimate goal to test the effects of different 16S regions sequencing in the same samples? If so, I would consider changing the sample names between the two runs so they are unique and instead add a metadata column that can group your samples based on 16S region. Merging a sample that has 2 different 16S regions sequenced is generally not a good idea. There’s some in depth discussions on this topic on the forum as you may have noticed. Just as a heads up!

[codea (Christian)]

these steps have worked perfectly.! thanks for your help!