Removing contaminating taxa from OTU table

Question

[kennylau.sg.air]

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!

[jotan]

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.

[kennylau.sg.air]

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.

Answer 1

[5heikki]

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

Answer 2

[kennylau.sg.air]

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.

Answer 3

[rahulgenexpress]

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.