Would it be possible to determine gene function ie function of other genes contributing to the microbiome from only 16S sequencing data using PICRUSt?
Great Answer! That's exactly what I was trying to find out. Functional patterns at the microbiome level need whole shotgun sequencing and interpretation needs to be done at a classical level to maintain a level of accuracy, other wise the subject matter could disappear into obscurity... In cases where very little is known it may be of use but taken with a significant tablespoon of salt is my understanding.
Wow thank you for that I am writing a paper on this and this will be a good source of information to draw from.
If you want to select the KO codes (KEGG Orthology database) that are interesting for environmental samples, you can extract this from FOAM database (http://cbb.pnnl.gov/portal/software/FOAM.html). And you can also do a new filter to keep only those which you are interested.
Good luck!
Slightly off topic but hopefully someone will answer. When you have all the .biom, .fasta files etc saved on a usb thumb drive and want to run the picrust scripts in Qiime (ubuntu) where should I save those files so that when running the script it is easy?
- Badges
- Science method