decontam
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benjjneb
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Dear all, I did amplicon sequencing (16S) from woodchip bioreactors that were used to clean water contaminated with pesticides. I am very new to the field and I am still...
Thanks a lot for the decontam package. i am extremely new to programming and i tried out decontam . i started with the "iscontam" function 1) The first graph is...
Dear all, In the reference manual, the isNotContaminant function is documented with one example: ` isNotContaminant(st, samdf$quant_reading, threshold=0.05)` Which I read as: seqtab = st neg = samdf$quant_reading threshold =...
Hi, I have an issue with running the frequency based isContaminant. I had a look at the other issues on here, but none of those suggestions solved my problem. My...
Hello Benjamin, I have two questions for you regarding the prevalence function in Decontam at ASV level. QUESTION 1: I assume that the control samples should be the same (resemble...
Hi Benjamin, I have came across an issue: When I use a certain method, I have been writing the table to a csv so I can look at which ASVs....
I was hoping to get some clarification regarding correct/appropriate use of your tool so that I am using it as it was intended. In particular, regarding the isContaminant and isNotContaminant...
Dear Benjamin Thank you for developing this user-friendly R package for the challenge with contaminant filtration. I have some questions about decontam below. I hope you have time for answering...
Hi, I encountered an issue when plotting frequency: `Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 605, 633` `In addition: Warning message: In plot_frequency(phyloseq_merged, taxa_names(phyloseq_merged)[c(1,...
I have recently read your paper very useful paper in Microbiome about identification of contaminants in metagenome sequence data. I would be very grateful if you could clarify for me...
