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.
biom-file conversion error.txt (7.2 KB)
Hello and welcome to the forum!
Could you share an example of how your 'otutable.txt' looks like? It will help to troubleshoot errors.
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 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.
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
Here are the examples of tsv tables to import to qiime2:
OTU/ASV/Feature table (columns are samples and rows are feature IDs):
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?
Here are the commands:
qiime tools import \
--input-path table.biom \
--type 'FeatureTable[Frequency]' \
--input-format BIOMV210Format \
qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-path taxonomy.tsv \
Thank you so much @timanix
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