I am trying to combine two biom (and qza) tables together. The issue that is coming up is that there are several duplicate taxa rows. For instance, I get two rows with Ruminococcus torques. Does anyone have an idea what is causing this? I inputted everything into Excel and the names are duplicates which means that there is not an invisible space or difference in capitalization. I have tried to convert the biom files into txt and then into qza files. I merged the qza files and I am still getting the same result–two rows with the same feature ID. Any help will be greatly appreciated!
Without specific commands run and outputs observed, it is hard to say. But, at first glance, this isn't surprising to me at all, for one reason: multiple features can have the same taxonomic identification.
Duplicate feature IDs shouldn't be possible - can you please share more specific information?
I made sure that that there were no invisible characters or spaces between the rows. Excel showed that they were duplicate rows. Thus, I was very confused why the qiime command was not putting them together.
Both biom tables were exported from MEGAN5. I was never able to figure out how to solve it with QIIME. So I had to put everything in excel and then take the greatest value out of the duplicate rows. Not the most efficient way still.
Hi @SterlingWright2016 - we do not provide support for QIIME 1 on this forum - QIIME 1 was discontinued January 1st 2018 and replaced by QIIME 2. If you would like to use QIIME 2 to perform the collapsing step, please see this command:
