Hello! I am trying to characterize communities of eukaryotes living in biofilms using V4 region 18s amplicon sequencing data. Working with this type of data is new to me, and very interesting!
The SIMPER analysis from vegan package in R intrigues me, as it would be amazing to know if certain organisms are found in one of my sample groups and not the others, or if any are found in only one location, for example. Because of eukaryotic gene duplication, I am considering ASV's, presence/absence rather than reads (though sometimes also relative abundance in certain situations), and doing my diversity measures with a binary Jaccard index. I know that SIMPER is based on the more statistically robust Bray-Curtis index, which I can't use with the type of 18s amplicon data I have. However, I have also read that Jaccard and Bray-Curtis are equivalent when only presence/absence is concerned. My question, ultimately, is whether it is possible to use SIMPER with binary distance matrices, and if it would be possible to use SIMPER with ASV data.
Thank you so much for your time!
SIMPER reads in a community matrix (presence/absence and abundance) and not a distance matrix. The latter is computed during the procedure. vegan's help file on the simper function is pretty clear re. this. Because I am not a geneticist, I cannot comment on the use of ASV data vs reads.
I hope this is of any help.
- Badges
- Science topic
- Similar topics
- Agricultural Science
- Agronomy