decontam
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benjjneb
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Dear Benjamin, I am reposting issue #83. I have the following set of samples (16S rRNA reads), which were sequenced together on the Illumina (MiSeq 2 x 300 bp) platform:...
Hi Benjamin, I have the following set of samples (16S rRNA reads), which were sequenced together on the Illumina (MiSeq 2 x 300 bp) platform: Soil: extracted/PCR/sequenced samples containing soil...
I have run decontam on a data set that has ASV’s for tumor tissue, negative controls, and control tissue. The negative controls did not have any tissue but only reagent....
Hello, first of all thank you for putting this package together. My lab is doing some metagenomics analysis on biological RNA-Sequencing samples and the only negative controls we have are...
Hi I am trying to use decontam on my data and I keep getting this error: Error in isContaminant(physeq2, method = "frequency", conc = "quant_reading") : Some batches contain zero...
Hello, I am having issues following the instructions laid out on the decontam website. I have generated a phyloseq object - "ps2". When I go to make a graph with...
I'm attempting to use the package decontam to filter out contaminants found in my negative controls. I followed the introductory tutorial, and created an OTU table (rows = samples, columns...
Thank you for this package - I've been enjoying going through both the package documentation and the paper. I have 130 samples in three batches (three different extraction sets with...
Dear All, I am looking at the Decontam vignette but I am stuck at the beginning where you read in the data with the following code: > ps
I’m slightly uncertain which DNA measures are optimal for the frequency based method (especially in case of samples containing animal tissues, where the proportion of microbial to animal DNA is...
