Dear Biostar Community,
I have a bunch of samples that resulted to be contaminated. Given that I exactly know which is the contaminant specie (which is present, with high abundance, in the OTU table) what is the most 'correct' way of removing it from the sample?
Should I just remove all the reads associated with the contaminant and re-normalize the OTU table?
Thank you!
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written
by
kennylau.sg.air •
3 answers
OTU table is not a standardized format. I presume you're talking about a file produced by QIIME. If this is the case, then you should use the QIIME script titled filter_taxa_from_otu_table.py
Hi 5heikki, thanks for your answer. filter_taxa_from_otu_table.py in QIIME does the job well. It is what I needed! Thanks so much.
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written
by
kennylau.sg.air •
Hi there,
There are ways to remove it efficiently, you should have its OTU/ASV id with you.
One could use filter_taxa_from_otu_table.py command by qiime
OR
If you are using phyloseq then go for prune_taxa function. this works best for me
AND to take are of other contaminated sequences, you can use recently developed package decontam
Hope this would help you.
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written
by
rahulgenexpress •
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I'm not sure I understand. If the sequence is aligned, why are there "contaminating" sequences? It seems to me that 'contaminants' would fail to align.
Hi Jotan, thanks for your answer. By contaminating I mean that I know that the specie 'X', which is present in the OTU table, has been introduced due to contaminated reagents. I would now want to remove such specie from the OTU table, ensuring that I am not distorting the data in any way
PS: I have edited my original question to make it more understandable. Thanks.