module load singularity/3
/workspace/hraegb/singularity/qiime-2019.7-picrust2.sif picrust2 full-pipeline
to obtain the KO.qza, PA.qza, EC.qza files. Then I was able to visualise them, as well as extract the biom data to tsv. Core diversity etc worked. I have two queries
The KO had IDs from KOOOO1 to K19789. There is a script to add descriptions and levels of the pathways here, but that does not work in the plugin.So then how do we annotate them and do the level wise analysis?
What is the best way to analyse the data? I have attached here the tsv for a look. extracted-KO-feature-table-biom.tsv (759.9 KB)
Also is it possible to look associate OTUs with the functional pathways at all within this plugin or do we have to use the full picrust?
I would really appreciate your help.
Thanks very much
I am pinging @gmdouglas to see if he can help. Thanks in advance!
Thanks very much @gmdouglas and @Nicholas_Bokulich for your prompt responses . I will have a go at the full version now. If I have any problems ( I am sure I will have some issues !), I will get back to you.
Hello again @Nicholas_Bokulich @gmdouglas
We have now installed picrust2. However I am stuck at the very first step of the pipeline
My question is
How do we generate the .fna for this work? The NGS analysis output were fastq.gz files which were then imported via PairedEndFastqManifestPhred33 format to get paired_end_demux.qza, that was then DADA2 processed to get repseqs.qza and table.qza; with the latter being converted via biom method to biom.
So I have the biom but not the .fna files for this script.I see that the study sequences are representative OTUs and/or ASVs under the typical workflow but I do not have any .fna outputs.
picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1
The “repseqs.qza” file corresponds to the actual ASV DNA sequences, which you can export to FASTA format.
Edit: Make sure that you read through the tool tutorial, which describes these input files: https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.3.0-beta)
Hello again @gmdouglas
Thanks so much. It worked. For benefit of others, who may be stuck here, this is what I did…
qiime tools export
module avail picrust2
module load picrust2/2.3.0
add_descriptions.py -i $PIC2/picrust2_out_pipeline/EC_metagenome_out/pred_metagenome_unstrat.tsv.gz -m EC
add_descriptions.py -i $PIC2/picrust2_out_pipeline/KO_metagenome_out/pred_metagenome_unstrat.tsv.gz -m KO
add_descriptions.py -i $PIC2/picrust2_out_pipeline/pathways_out/path_abun_unstrat.tsv.gz -m METACYC
Thanks very much once again,
hello sir，I want know how did you do the downstream analysis？
Hi, I am interested on how did you move forward for the downstream analysis of your dataset? Especially on the enrichments? Thank you, hoping you could share more on this!