Picrust 2 KO abundance

Hi Everyone, I am facing problems in KEGG pathways abundances from the predicted KO abundances. I got the output file which is shown here: pathway_out_pipeline/KO_metagenome_out/pred_metagenome_unstrat.tsv.gz.

I am facing problem in getting the KEGG pathway output file. Kindly Suggest me the code which takes unstrap.tsv.gz file as a input file.

Hi, Upasana!

Have faced the same problem recently:

  1. Unzip the file using
    gunzip pred_metagenome_unstrat.tsv.gz
  2. Convert tsv to biom using biom:
    biom convert -i pred_metagenome_unstrat.tsv -o converted_table.biom --to-hdf5
  3. Import data into qiime2
qiime tools import \
--type FeatureTable[Frequency] \
--input-path converted_table.biom \
--output-path ko_predicted_table.qza \
--input-format BIOMV100Format

Proceed with analysis using QIIME2.

Cheers.

Thanks for your suggestions.

But I am still facing a problem, I have used the QIIME 2021.4 version to carry out the rest of the analysis. And for using q2-picrust 2 plugin i need to install 2021. 2 because the q2-picrust 2 plugin of 2021.4 version is not available as of now.

if you could provide furthers details on using the PICRUST 2 standalone version for carrying out KEGG pathway for KO Abundance. Kindly provide here.

Hi Upasana,

yes, the picrust was not yet updated to the recent version of QIIME2. The issue is open on GitHub.
On GitHub Wiki you may find instructions on how to use PICRUSt2 as a standalone in a separate environment.
I assumed, that you've already been past this step, as you've obtained the output from PICRUSt2.

Cheers

Yes, I have used Picrust 2 standalone version to carried out the analysis and from that only I got pred_metagenome_unstrat.tsv.gz file. and I have followed the process that is available in FAQ section but their the code is written for the files in the stratified form and I got in unstratified form. so, I am not getting any idea, how to proceed further to get appropriate results.