combination differnt dada2 result

User Support
1

Hello, I am working on a meta-analysis task and I want to combine 3 different datasets with the following command: Usage: qiime feature-table merge [OPTIONS]

Combines feature tables using the overlap_method provided.

Inputs:
--i-tables ARTIFACTS... List[FeatureTable[Frequency]¹ |
FeatureTable[RelativeFrequency]²]
The collection of feature tables to be merged.
[required]
Parameters:
--p-overlap-method VALUE Str % Choices('average',
'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum')¹ |
Str % Choices('average', 'error_on_overlapping_feature',
'error_on_overlapping_sample')²
Method for handling overlapping ids.
[default: 'error_on_overlapping_sample']
Outputs:
--o-merged-table ARTIFACT FeatureTable[Frequency]¹ |
FeatureTable[RelativeFrequency]²
The resulting merged feature table. [required]

I had two questions
How and with what method does this command combine different datasets (--p-overlap-method VALUE Str % Choices('average',
'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum')¹ |
Str % Choices('average', 'error_on_overlapping_feature',
'error_on_overlapping_sample')²), and in the second question, is this correct?

2

Hello @Rm733,

When your tables have overlapping samples and/or overlapping features, you can choose what you want to happen:

'average', output the average value of the features with the same ID
'sum', output the sum of the features with the same ID
'error_on_overlapping_feature', throw an error if two features have the same ID
'error_on_overlapping_sample', throw an error if two samples have the same ID

Do you have the same sample IDs across your three tables?

Do you want to average your features, or add them up?

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