Preparation of input file.

[kohei-108]

Hello.
I have metagenome fsatq files.
How can I analyze files by converting them?

thanks.

Kohei

[asmvernon]

Hi Kohei,
You have to first annotate the metagenomes with KEGG orthologs (K numbers). PICRUSt could be a useful tool for that. Have a look at this tutorial: http://picrust.github.io/picrust/tutorials/metagenome_prediction.html#metagenome-prediction-tutorial

Once you have the list of K numbers, you can use the function query_genomes_to_modules( ).

Best,
Andrea

[kohei-108]

I have metagenome sequences, not a 16S rRNA sequences.
Can PICRUSt annotate metagenome sequences?

[asmvernon]

Hi,
You do seem to need the 16S sequence (sorry, I have no experience annotating metagenomes).

This tutorial could walk you through using prokka to annotate the metagenome sequence. Once annotated, you could use the amino acid sequence(s) to annotate it with K numbers (https://www.kegg.jp/blastkoala/, https://www.kegg.jp/ghostkoala/).

However, as I mentioned, I don't have any experience with this type of datasets, so below are some papers and tools I have come across, which might help guide you better.

PAPERS AND RESOURCES
NCBI: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ (using the WGS mode/option).
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0176469
http://metagenomics-workshop.readthedocs.io/en/latest/annotation/quantification.html
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892715/
https://www.nature.com/articles/srep19233
https://www.nature.com/articles/ncomms11257

[kohei-108]

Thanks!

[asmvernon]

Hi again,
Just came across this paper that could also be useful to you:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1116-8
:)

[kohei-108]

Thank you!!!
I'll read this paper.