losing sample when importing biom

[taf1g17 (Tom Freer)]

Coral-core-import.csv (6.1 KB) Hello,
Please help. I am trying to import an excel table into a qza but repetitively lose a sample during import/conversion.
I start with the excel feature table (Coral-core-import.csv) and convert to .tsv (Coral-core-import.tsv) or into .txt (Coral-core-import.txt) using google sheets. This tsv/txt file still has all samples.
I then convert this .tsv into .biom using:
biom convert -i Coral-core-import.txt -o Coral-core-import2.biom --to-hdf5 --table-type="OTU table" --process-obs-metadata taxonomy
or using:
biom convert -i Coral-core-import.tsv -o Coral-core-import.biom --to-hdf5

both commands above work for the conversion, however when I then attempt to import the .biom file, the import works however I lose a sample from the table and all corresponding values. I am using:
qiime tools import
--input-path feature-table-v100.biom
--type 'FeatureTable[Frequency]'
--input-format BIOMV100Format
--output-path feature-table-1.qza
and
qiime tools import
--input-path feature-table-v210.biom
--type 'FeatureTable[Frequency]'
--input-format BIOMV210Format
--output-path feature-table-1.qza

Please could someone help (preferably without just referring me to another forum post/web page if possible as I have spent too many hours scouring the internet for a fix and I simply cannot work out what is going wrong) - thank you so much guys.

Coral-core-import2.qzv (393.6 KB) Coral-core-import2.qza (9.9 KB) Coral-core-import2.biom (44.2 KB) Coral-core-import2.txt (6.1 KB) Coral-core-import2.txt (6.1 KB) Coral-core-import.qzv (393.6 KB) Coral-core-import.qza (9.9 KB) Coral-core-import.biom (43.7 KB) Coral-core-import2.txt (6.1 KB) Coral-core-import.csv (6.1 KB)

[andrewsanchez]

Hi, @taf1g17,

If I understand correctly, you want to convert a file to a biom table and then create a qiime 2 artifact directly from that .biom file. Is that correct?

I have a few questions:

• The value you passed to -o (Coral-core-import2.biom) doesn’t match up with the values passed to --input-path (feature-table-v100.biom and feature-table-v210.biom) on the qiime tools import command.
  • Are you sure you are importing the correct files?
• Can you explain why you suspect that you are missing a sample? How did you determine that?
• You attached multiple, seemingly duplicate files to your post which make it a bit difficult to know what you did. Can you clarify how we should go about reproducing your issue? For example, neither of the input files shown in your example biom convert commands, (Coral-core-import.txt and Coral-core-import.tsv) were attached; the attachments had similar names. This makes me unsure whether or not I am reproducing your exact states. I want to be sure I am testing this on the exact data you used.

Thanks, and sorry for the late reply!

[taf1g17 (Tom Freer)]

Hello,

That is correct, however I was actually making some foolish mistakes and I was able to use the actions in Feature frequencies per sample to achieve what I was after - Thank you though!!

Tom