Mothur output files for PICRUST2

[A Cupples]

Can anyone provide advice on how to create input files for PICRUSt2 from Mothur? Thanks in advance. 

[Gavin Douglas]

Hi there,

SPF files can actually be used as input. In addition to this table you would need a FASTA files of all OTUs output by mothur - I’m not sure what the mothur OTU sequence format is, but FASTA format is quite simple - you can see the tutorial for an example of what it looks like.

Cheers,

Gavin

On Apr 20, 2021, at 10:17 AM, A Cupples <cuppl...@gmail.com> wrote:

Can anyone provide advice on how to create input files for PICRUSt2 from Mothur? Thanks in advance. 

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[Khalid IBRAHIM]

Dear Gavin,

I hope you are doing well and safe.

I wonder if I can get the files of custom code for Feature ID (sequence) to identify for each taxon data for analysis the path_abun_contrib.tsv such as

009a0df71afeb8bfa9ba578f5a804573 & 02bb810252afc5b6121d3c42fa55814f

Thank you in advance

Cheers

Khalid

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[Gavin Douglas]

Hi there,

Sorry I'm not sure what you're referring to - would you mind reminding me?

Thanks,

Gavin

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[Khalid IBRAHIM]

Hi Gavin,

thank you for your reply

I find some taxa on data set in the link below  for example 0ae2ea78213ca741ded6f9b30042d4b1 d__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes_hadrus

data/taxonomy.tsv · fe32a9f1a199af0cdfa8b6dd4abce7b7d1b586d6 · Benoit Goutorbe / stool-preservation · GitLab (inserm.fr)

but unfortunately I didn't find some of them such as 009a0df71afeb8bfa9ba578f5a804573 & 02bb810252afc5b6121d3c42fa55814f

Wonder If any further information

Cheers

Khalid

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[Gavin Douglas]

Hi there,

I’m not sure what you’re asking exactly. If this is about taxonomy classification, then that’s no related to PICRUSt.

Are you asking about those ids because they are not found in the path_abun_contrib.tsv file, is that what you mean? That can happen if they are filtered out due to the placements being above the max NSTI cut-off, which is 2 by default. But I’m not sure if that’s what you’re asking about.

Cheers,

Gavin

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