PICRUST 2 standalone version

Other Bioinformatics Tools
#1

Good Evening to all the members! I am new to this platform, Currently I am using QIIME 2 2020.11 version and I want to analyze my results in PICRUST2. As of my knowledge, there is no such compatible q2-picrust2 plugin for 2020.11 qiime 2 version. so, I have shifted to standalone version of PICRUST 2 for doing KEGG pathway analysis where I am facing problems related to seqs.fna and .biom files as these file are not supportable to qiime 2. So, if anybody has any information related to this issue. Please help me out to how to proceed further.

Thanks & Regard
Upasana Gupta

#2
#3

Hi @upasana127, welcome to :qiime2:!

If you would like to import your biom and fna files please see the Import data documentation. I’d highly recommend that you read through the Documentation and Tutorials to help find your footing. :slight_smile:

Cheers!

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#4

Sorry for the late reply!
I want to use Picrust 2, for that i need seqs.fna, featuretable.biom and metadata.tsv files but as mentioned in the above post I have used qiime 2 2020.11 from where i got seq.qza and table.qza files format as my qiime 2 output files and these files format are not compatible with standalone version of Picurust2. So, kindly suggest me how can I achieve that goal for using picrust2

#5

Hi @upasana127, sorry I misread your post I though you were trying to import files. Sorry about that. :man_facepalming:

Without knowing what specific errors you are running into, make it difficult to help. According to the PICSRUSt 2 docs it should read biom and fna files just fine. Unless they are using a different version of biom? You can try running biom convert to re-format your biom table to suite your needs. :building_construction:

I’ve not used the stand-alone version of PICRUSt 2 myself. Hopefully, others on the forum can be of help. Otherwise, you may be better off asking the PICRUSt 2 devs, or simply install an older version of QIIME 2 in which to run q2-picrust2. I tend to keep several versions of QIIME 2 on my machine for instances like this.

-Good luck!
-Mike

#6

Thank you so much for your time and suggestions!
I will try to install a different version for this matter.

Thanks again!

Thanks
Upasana Gupta

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#7

Not problem @upasana127!

Oh, I should have mentioned that QIIME 2 has biom as part of the standard install.

Good luck!

-Mike

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#8

you need to export the qza files using “qiime tools export”, which will give you biom table to use as input for PICRUST2.