Picrust 2 metagenomic prediction

[BHAGYASHRI PODDAR]

Hey there,

I wanted to know that what command line I have to follow for metagenomic prediction of picrust 2 output. I have ran the picrust2 command line 

picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1

Now what next???

[Robyn Wright]

Hi there,

You can see a couple of suggestions within the PICRUSt2 tutorial page here, but really, you can analyse the output in any number of ways - as you can for the initial output of amplicon sequencing studies. How you will want to analyse it will depend on the questions you're trying to answer with your dataset, and what you were looking for by performing the PICRUSt2 analysis, i.e., do you want to know whether the overall functional profiles differ between sample groups, or were you more interested in particular functions or pathways within those samples? Unfortunately no one else can answer those questions for you, but you can see some tools that you'll be able to use to explore your data in the tutorial page.

Best wishes,

Robyn

[BHAGYASHRI PODDAR]

hi there,
I have ran the command for categorizing the picrust2 output to higher level using below command
pathway_pipeline.py -i KO_metagenome_out/pred_metagenome_strat.tsv -o KEGG_pathways_out --no_regroup --map picrust2/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv
and it was successful.
Now my question is how can I convert this KEGG_pathways_out file to KEGG pathway to run in the STAMP.

Thanks and Regards,
Mrs. Bhagyashri Poddar Raut
Ph.D. Scholar,
Environmental Biotechnology and Genomics Division (EBGD),

CSIR-National Environmental Engineering Research Institute, 

Nagpur-440020

Mobile: 08793486044

bhagyash...@gmail.com

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/c694a3f8-fa64-4399-a71e-ed709b3d91d6n%40googlegroups.com.

[Rashmi Ira]

Hello All,

I am new to picrust/picrust2. I am working with QIIME2 data analysis and want to perform functional annotation using Picrust2 plugin. First of all I want to train my classifier for V3-V4 region with 99% identity. I tried to check files from http://ftp.microbio.me/greengenes_release/2022.10/ new release of GG-2022 but confused that which file is of my use!!! Please help me out for this, so that i can start my further data processing and analysis.

Any help will be appreciated.

Best Regards,

Rashmi Ira

[Robyn Wright]

Hi Bhagyashri, 

Did you also look at the STAMP example page? I have not personally used STAMP, but it looks like you used the stratified file as input for regrouping to pathways, and STAMP probably requires the unstratified file. 

Note also that you could try using JarrVis - a tool that someone else in our lab has been working on - for visualising the stratified file, although you will likely need to carry out some additional filtering beforehand. 

Best wishes,

Robyn

-----------------------------------------
Dr. Robyn Wright (she/her)
Mitacs Post Doctoral Fellow
Langille Lab
Dalhousie University (Canada)

Dalhousie University is located in Mi’kma’ki, the ancestral and unceded territory of the Mi’kmaq. We are all Treaty people.

[Robyn Wright]

Hi Rashmi,

I just wanted to note that this group is actually for using PICRUSt2, not QIIME2 - QIIME2 has a separate forum here. I am, however, able to answer your question.

You can find some classifiers already available for download here - we have not really found it to make a difference whether we use the full-length classifier or one trained on only the region of interest. We do also have an example of the commands required to train a taxonomic classifier here. 

Best wishes,

Robyn

-----------------------------------------
Dr. Robyn Wright (she/her)
Mitacs Post Doctoral Fellow
Langille Lab
Dalhousie University (Canada)

Dalhousie University is located in Mi’kma’ki, the ancestral and unceded territory of the Mi’kmaq. We are all Treaty people.

[Rashmi Ira]

Hi Robyn,

Thanks for writing back. I know this forum is for PICRUSt2, actually I have already performed my most of the analysis using Silva, but for using PICRUST2 as per my knowledge we have use GG based annotation. That's why I asked this question here, anyways that you for your kind response. I will look into the Provided links. 

Best regards,

Rashmi Ira 

You received this message because you are subscribed to a topic in the Google Groups "picrust-users" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/picrust-users/O59XqEsXth4/unsubscribe.
To unsubscribe from this group and all its topics, send an email to picrust-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/a366d14e-a1ab-4bca-8250-e7694b92dc31n%40googlegroups.com.

[Robyn Wright]

Hi Rashmi,

The first version of PICRUSt did require classification using the GreenGenes database because it was based on the taxonomy ID's that linked to that. Version two does not require classification with any particular database (or any classification at all) - only that you have a feature table with taxa ID's that match a fasta file with those sequences.

Best wishes,

Robyn

[Rashmi Ira]

Hi @Robyn 

Thank you for your kind response. I will look into it. 

Thanks a lot. 

Best Regards,

Rashmi

To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/592592f3-7378-45ba-8e51-a0a814242a38n%40googlegroups.com.