decontam
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benjjneb
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Hi, I need some help with my analysis. I'm trying to plot the frequency of contaminants with Decontam but I have some errors: Error in data.frame(..., check.names = FALSE) :...
Hello, I am trying to figure out what is wrong with my analysis. I am trying to decontaminate this dataset ``` phyloseq-class experiment-level object otu_table() OTU Table: [ 4723 taxa...
210 samples were sequencing in my research. And the number of sequencing reads of my sample was varied greatly, from 40,000 to 210,000. Also, the number of sequencing reads was...
hello .. I went for the prevalence method; my plot using this command is different from the one in the tutorial (having just few as you can in the below-attached...
Hi I am very new to this so I might have some very basic questions to ask. I have quite a lot of contamination in my control and am therefore,...
Hi, I am trying to figure out quant_reading for my samples. Here is what I am thinking: 1) Where does it come from? Use qPCR data as my quantification. My...
Hi, I'm new in microbiome analysis and R. I have low biomass samples from mosquito's midgut. I have two negative controls (one blank from DNA extraction, and one from PCR)...
Hi there, I'm very excited to try using `decontam`, but I'm not sure it'll work with our data. I'd be grateful for any advice. I've got the following `phyloseq` object...
Hello I am looking for advices for the best way to clean up microbiome sequencing data that have been contaminated by Mock community (Zymo) controls. I know how many cells...
Recently I have been exploring the `plot_frequency()`-function in a bit more depth and I found two issues: 1. Sometimes the function yields an error when the `neg`-parameter is set (this...
