Hi Ana,
Can you give me some details about what kind of data you’re working with? Kraken is most commonly used with metagenomic data, in which case you don’t need to predict functions (what PICRUSt is used for), because you can just annotate the functions within your data. In this case, I would recommend following our labs Metagenome workflow here.
If your data is 16S amplicon sequencing, it doesn’t really matter which method you have used for taxonomic classification as what you need for PICRUSt is your ASV/OTU sequences and a table with the abundance of these sequences across your samples. You can see descriptions of these files here.
Thanks,
Robyn
--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
picrust-user...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/picrust-users/ff1af959-826b-4253-b581-e58dac1bcae3n%40googlegroups.com.
Hi Ana,
I’m not familiar with any workflows that use Kraken for taxonomic assignment, but usually in amplicon analysis (e.g. our lab workflow here) you would:
Usually it would be the sequence file that you have at the end, where the rare, contaminant and unclassified ASVs have been removed, that you would use for input into PICRUSt2. If you have details of your workflow (all of the commands that you run) then maybe I can advise better.
Robyn
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/a5c4c2d5-ac9b-42c1-ba78-a3cb13eac538n%40googlegroups.com.
Hi Robyn,
Thanks. I use Kraken2 in my pipeline with the following command:
kraken2 --use-names --db $DBNAME --threads 24 --report name.report
Ana
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/AS8P191MB14296C709D3E1AEF688DF8AEF8B8A%40AS8P191MB1429.EURP191.PROD.OUTLOOK.COM.