Biom and Fasta file have mismatch ID in PICRUST2

Integrating mothur with other programs
1

Hi,

I have processed my 16S V4 paired-end sequence data using the mothur SOP in version 1.47.0 and now am on the analysis stage. I want to run my mothur output biom and fasta files through PICRUST2 to take a look at the predicted functional abundances. However, I have found that the fasta file contains sequence IDs that look like this: >MISEQ_159_000000000-JJ3F9_1_1106_9289_25841 and the biom file only contains the OTU IDs (Otu00001) so there is an ID mismatch between these files and therefore it won’t run in PICRUST2. Do you know how I can get the IDs to match up?

Thanks in advance.

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I think you might need to use get.oturep to get a representative sequence for each OTU - use the abund approach. This will give you a fasta file with the OTU number as the sequence name.

Pat

1 Like
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Thanks for your suggestion. I’ve made the fasta file using get.oturep with the abundance method and removed the sequence IDs as they were still in the file and am now left with the OTU number for each sequence. I’ll run the PICRUST2 pipeline and see if it completes.

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