converting text file to biom file issue

[Rishikesh12 (Rishikesh Dash)]

I have an OTU table in the excel format. I want to convert it into biom file.
-> first i saved excel format file in text(tab delimited) file format.
-> then i used 2-3 different commands to convert .txt file to .biom file
-> but it is throwing errors.
-> please help me how i can solve my errors. i am attaching error file.

All response are invited.

Thank you
Rishikesh Dash
biom-file conversion error.txt (7.2 KB)

[timanix (Timur Yergaliyev)]

Hello and welcome to the forum!
Could you share an example of how your 'otutable.txt' looks like? It will help to troubleshoot errors.

[Rishikesh12 (Rishikesh Dash)]

Thank you for response.. I am attaching the otutable.txt snap below

please look at the picture and help me out from the problem.
Thank you

[timanix (Timur Yergaliyev)]

Thank you for sharing.
In Qiime2, taxonomy information usually stored in a separate file from OTU table. So, feature table in Qiime2 - it is just OTU/ ASV counts. I suggest you modify table so it would have OTU ids as rows and samples as columns with counts as their values.
For taxonomy files, you should prepare a second table with two columns - Feature ID (OTU ids) and Taxon (all taxa levels from kingdom to species / genera, separated by ";").
Let me know if if you will need help with importing commands.

[Rishikesh12 (Rishikesh Dash)]

Thank you for sharing the information. So i will make two biom file : one tax file and another is otu file.
can you please share a picture of both of file that will help me a lot to understand that how i can do two separate file for my own data.
Thank you so much
@timanix

[timanix (Timur Yergaliyev)]

Hi!
Here are the examples of tsv tables to import to qiime2:

OTU/ASV/Feature table (columns are samples and rows are feature IDs):

Taxonomy file:

[Rishikesh12 (Rishikesh Dash)]

I have successfully imported feature table..
can you tell me one thing is command are same for converting taxonomy file and please share commands for importing taxonomy file. I have searched for taxonomy file importing commands but don't found where it is?

Thank you
Rishikesh

[timanix (Timur Yergaliyev)]

Here are the commands:

qiime tools import \
  --input-path table.biom \
  --type 'FeatureTable[Frequency]' \
  --input-format BIOMV210Format \
  --output-path table.qza

qiime tools import \
  --type 'FeatureData[Taxonomy]' \
  --input-path taxonomy.tsv \
  --output-path taxonomy.qza

[Rishikesh12 (Rishikesh Dash)]

Thank you so much @timanix

Rishikesh