I am sorry, because I am reposting this query again, because I thought I have posted in wrong place.
Please ignore mistakes.
After performing the taxonomic and functional analysis of Shotgun dataset in Metaphaln and humanN, I have got my data in terms of relative abundance. I have also got biom files for each data sample:
Can we convert the biom files into OTU table and then use in R for different downstream analysis.
If so, please help me with:
- Do i need to combine the biom files first
- I need the code to convert the biom to OTUs. Tsv file
Thanks ans Regards
Thanks, I converted the biom to Tsv using biom convert command.
However, I have still one issue that is:
As Metaphlan doesn't generate OTUs rather it gives relative abundance. But how can I get the OTUs for diversity analysis.
Any way to get it done
Thanks and Regards
I searched through the forum and found a plugin
Error in Import · Issue #13 · gregcaporaso/q2-sapienns · GitHub
I successfully installed the plugin and tried withy my dataset, but got the error
I then tried to run the command qiime tools import --input-path Galaxy.tsv --output-path Galaxy_outPut.qza --type MetaphlanAbundanceTable and got the error
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/result.py", line 250, in import_data
output_dir_fmt = pm.get_directory_format(type_)
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 354, in get_directory_format
TypeError: Semantic type MetaphlanAbundanceTable does not have a compatible directory format.
An unexpected error has occurred:
Semantic type MetaphlanAbundanceTable does not have a compatible directory format.
See above for debug info.
I am also attaching the file , the analysis was carried out in Galaxy using Metaphlan
I found that the functionality was developed for the MetaPhlAn format that contains exactly two columns (
NCBI_tax_id ) before the sample abundance columns, but should also work if the
NCBI_tax_id is not present (as is the case in MetaPhlAn 4 output). I recommend looking at the column headers for the first three columns in your input file before attempting to use this code:
But then I have one query here, how can we use this at different taxonomic levels (like phylum, class....)
thanks and Regards