I have microbiome sequencing data and I have analysed it to determine which taxa are up or down-regulated with my treatment, however, this doesn't really tell me much about the metabolic changes.
Is there anything I can use that is similar to the Qiagen IPA where I can place my metagenomics data and it can tell me if there are any changes in metabolic pathways?
Any links and tutorials would be greatly appreciated!
You should have specified the kind of metagenomic data that you are having i.e. amplicon-based or shotgun. I am believing you are having 16s rRNA gene-based amplicon sequence data, for that you can use Tax4Fun or PICRUST2 for functional analysis. They are available on Git-hub, additionally for PICRUST2 basic "R" is also required.
https://www.nature.com/articles/s41587-020-0548-6?proof=t
https://www.sciencedirect.com/science/article/abs/pii/S0167701217301781?via%3Dihub
Have Fun !!
Hi,
For 16S rRNA gene-based amplicon sequencing data Tax4Fun2 and PICRUSt2 can be used for functional analysis. They are available with R program. PICRUSt2 plugin is also present in QIIME2.
Hi, Shi Li
I recommend you use Userarch (https://www.drive5.com/usearch/) or Dada2 (https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/upload/OtuUploadView.xhtml) and then take your zOTU/ASV and taxa table, generated by one of these programs and analysis on MicrobiomeAnalyst (https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/upload/OtuUploadView.xhtml).
Currently, I am working with service provision on bioinformatics analysis. If you are interested in contracting this type of service, you may contact me! If not, I'll be glad to be able to help around here.
Good luck!
Shi Li
Sorry!
Here is the link to dada2(https://benjjneb.github.io/dada2/tutorial_1_8.html)
Is there a minimal sequence depth or length of the sequence read (>xxx bp) required to use Tax4Fun2 and PICRUSt2?
- Badges
- Science method
- Similar topics
- Mathematics
- Statistics
- Statistical Modeling
- Analyses of Variance
- ANOVA