Can I perform an ordination method with the output of ANCOM? Can I get a standardized OTU table as output?

08 August 2018 0 5K Report

For my master thesis I need to look at the ciliate (protozoa) community of some sea water samples using 18SrRNA Illumina Sequencing. I analyse my data in R. I want to perform CCA or NMDS of my abundance data (OTU table) and the environmental parameters of the stations, that were sampled.

So I need to standardize my OTU table and I wanted to try ANCOM. But do I get an output I can work with in the ordination methods of R package vegan ?

Badges
Science topic

More Anita Sinner's questions See All

Biplot the individuals of PCA on abundance data and the variables of PCA on environmental data in R?

I found a graphic where someone used a PCA on abundance data and overlaid it with environmental factors of the sites, see the attached graphic of the publication ciliate distributions and forcing...

06 July 2018 8,651 0 View

Can I overlay the coordinates of variables of one PCA over the coordinates of individuals from a second PCA and still interprete the results?

I do have two sets of data: Abundance data and environmental data and need to "link" them or "overlay" them in a PCA: I want to conduct a PCA in R which gives me the individuals Ciliate species as...

06 July 2018 4,893 1 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View

To date, according to health authorities, 30% of the population's diseases are initiated by drinking water pollution. Do you know this problem?

The main studies are as follows: * regular and timely receipt of information about the state of the environment using automated systems (stationary and mobile); * operational analysis of the...

23 February 2021 912 5 View

Can I use FLEXBAR to detect and remove barcodes out of my short reads without demultiplexing ?

Hello, I have demultiplexed my short reads and I have removed the Illumina adapter left in the sequences and now I need to remove the barcodes used by the sequencing centre from my reads. I have...

22 February 2021 9,873 3 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

What is the significance of (isolated) high titers of IgG anti GD1a antibodies in an older patient with polyneuropathy?

Remote history of Campylobacter infection with reactive arthritis, and Spitz nevus (UMP). Arthropod exposure in Zika/ChikV endemic area prior to emergence of length dependent, sensory PN with...

18 February 2021 8,719 1 View

Repository for capture-seq raw reads?

I am a research tech in a wildlife genetics group and my PI and I are trying to figure out how/where to put raw reads in a repository. We have capture-seq NGS from Rapid Genomics. The post-doc who...

17 February 2021 7,575 2 View