Decontam results

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1

Hiya, running decontam on output from a qiime pipeline. Data is 16s skin microbiome. Got some interesting plots showing non-contaminants and contaminants and wondering if this looks right to people who have done this before? I feel like my noncontaminants are very sparse and my contaminants don't follow the red trendline as closely as they could. Also, does anyone know what the massive collection of black data points/dots at the bottom of all the graphs represent? for reference I generated my contaminant list with a higher threshold:
contamdf.freq <- isContaminant(ps, method="frequency", conc="quant_reading", threshold = 0.2)

Top "non-contaminants":

image
image1111×608 162 KB

"Contaminants":

contam
contam1723×961 315 KB

Thanks!

2

@jordenrabasco, Do you have any thoughts on this?

3

Hi @op9183 overall everything looks alight on the first pass. Your contaminants look like they are following the red line appropriately but it is hard to say for certain due to the size of the graphs. Could you expand more on what you mean by sparse? The dots at the bottom are 0s so those are samples where the ASV does not appear.

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