Functional Prediction - PICRUSt (Greengenes) - Tax4Fun (SILVA) using the QIIME outputs

[andrefc]

Hi everyone,

Can you advise on how to obtain the data from QIIME outputs in order to run the Functional Prediction - PICRUSt (Greengenes) - Tax4Fun (SILVA)?
I am trying to run using the Microbiome Analyst, but they cannot recognize the QIIME outputs. From Visual Exploration to Comparison and Classification I would read everything, but not the Functional Prediction.

[Yao]

Hello，
Generally，if you choose the correct database (Greengenes for PICRUST or SILVA for Tax4Fun) for the taxonomy assignment，MicrobiomeAnalyst can deal with the output.

If this is not the case, please follow our post guideline for specific trouble shooting.

Hope this helps.

[andrefc]

Hi,
I chose the Silva output to run the Tax4fun with the QIIME against SILVA database as Annotation Pipeline and this error came on the screen.
“Error Please check the taxonomy levels”

Also, I chose Greengenes OTU ID to run the Picrust. The following screen came out, the graph became empty with the attached output.
functionalprof_picrust(1).csv (692.7 KB)
picrust_ko_0-1.pdf (6.5 KB)

I would greatly appreciate it if you could advise me on how to run the PicRust. The input files are available upon request.
Thanks

[jeff.xia]

Please read and follow our post guide.

[andrefc]

Dear All,

Please find attached the screenshot of my procedures. In fact I could make the PicRust and found the log - KO counts (Slide 6). From now, can anyone show me the tutorial on how to access the metabolic functions using this graph? or table?
Also, I tried to run the Tax4fun but I found some error. Can anyone guide me on how to solve this issue?
Regards,
Presentation1.pdf (565.5 KB)

[Yao]

Hello,

You can us our SDP module to further analysis the result KO abundance table from PiCRUST following * Performing shotgun metagenomics data analysis (SDP).

Tax4fun works for the silva-based pipeline. I noticed that you upload the same dataset to Tax4Fun as to PiCRUST but only change the selection for the taxonomy labels. This is not correct. If your data was annotated using GreenGenes, it not fit for Tax4Fun.

Hope this helps!

[Mustafa_Elbakary]

I performed the PICRUST module, but I can’t find the output analysis. How can I find it?

[andrefc]

Dear All,

Concerning the use of PicRust to run the outputs from QIIME could you please provide me with any specific tutorial on that? Until now, I only succeeded in running the other analysis, except for the PCIRUST or TAX 4 fun.

[jeff.xia]

The requirement for PICRUSt is clearly indicated on the page (see below). It will not work if you have annotated your data using other libraries in QIIME.

Note MicrobiomeAnalyst offers a complete workflow:
Amplicon seq => Raw Data Processing (SILVA + DADA2) => ASV table => Marker Data Profiling (Tax4Fun2)