Good day and thanks for your help, i have two otu abundance table with difference samples name and taxa attached, i already converted the to .biom files and imported them into qiime2 artifact (.qza), however after i tried to merge them i got the following error:
--i-tables feature-table-1.qza feature-table-2.qza
Plugin error from feature-table:
No solution for inputs: (List[FeatureTable[RelativeFrequency] | FeatureTable[Frequency]], Str % Choices('error_on_overlapping_sample')), check the signature to see valid combinations.
Debug info has been saved to /tmp/qiime2-q2cli-err-q_79vm22.log
i do not know what is wrong with my feature tables, attached are the .qza files format used with taxonomy at the last column.
Need your help!!!!!
Good day, i am back again, i have three (3) different otu tables in .txt files that i need to import and merge them into one otu for analysis, each otu table has different sample names that i want collapse OTUs with identical taxonomy. I was in this forum that i need to separate taxonomy information in a separate file from OTU table before importing and coverting to .biom file. how can i merge this otu tables with different sample Id. attached are the examples of my otu tables
Thank you for your help.
@Zango, it looks like you are trying to merge a
FeatureTable[Frequency] with another of type
FeatureTable[RelativeFrequency] which cannot be combined in a meaningful way, you will want to feed the artifact of type
FeatureTable[Frequency] through this tool to convert it to
[RelativeFrequency] so that they can be meaningfully merged. After you have all of your OTU's collected, you can then annotate them with taxonomic information to them as seen in the Parkinson's Mouse tutorial.
Thank you very much for your reply, basically all the tables are the otu tables, i don't know why it is showing this error, i am really lost the otu are from different parts of plant parts which need to be merge, their taxonomy are entirely different. I need to merge them to check core otu among different plant compartments how can i use the taxonomic information? i should import two taxonomic files? i am lost
It is because of the differences with how the abundances are measured in each of your tables. Check out this page for a discussion of the differenences between the two, and then you can use the
feature-table relative-frequency tool (docs) to convert tables with raw abundances to relative abundances, then you can use the
feature-table merge tool (docs) to combine them. Hope that answers your question!
Thank you very much for your help Sir, Keegan Evans, i have successfully merged the files, Thanks and God bless
i am back Sir, after I merged the OTU tables I discovered that many OTUs were with the same OTU but their taxonomic informations are not the same, since my tables are from the same plants but at different phase of growth, i really don"t know how to collapse the taxonomic information for each data set for proper annotation. i found an article (COREMIC: a web-tool to search for a niche associated CORE MICrobiome) using the same QIIME to collapsed and merged their different OTU tables but i don't know how to deal with the same OTU number but different taxonomic info. Need your help
I think part of the problem is that you have duplicate OTU labels in your different data sets, which is (I think) why you are getting different taxonomic annotations for the same OTU labels in your merged table. I think collapsing the taxonomy information of the current merged table would be worse than unhelpful, which is just as well as unfortunately the
taxa collapse function only works with data stored as
FeatureTable[Frequency] rather than
I think the best way forward might be to start over with a re-import of your data. There are a couple of different ways that this could be helpful.
The first is to import each of your datasets twice, the first time as
FeatureTable[Frequency] artifacts and again as
FeatureData[Taxonomy], then use these pairs to run
taxa collapse(here are the docs),which will create unique ids and get the taxonomic collapsing you were after, then convert/merge as you already have.
The second is to import as before, then use
feature-table rename-ids(docs) to give each feature a truly unique label, convert/merge as necessary, and then do a taxonomic assignment(an example here), and carry on with your analysis.
Hope this is helpful, and sorry for the long reply, there has been a bit of behind the scenes discussion of how to handle this.
Thank you very much, i am really grateful, you people are blessing to us
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