When working with eDNA we sometimes face some contamination, and it may lead to false-positive or negative, and I think if some of these cases, it creates a problem, or it may be interpreted as a grown on robustness, cause if we are using universal approach, we should be capable of finding any DNA sequences, like human DNA contamination, so what do you think about it?
I can't get exactly what you wanted to ask... but if you are dealing with bacterial sequences and you have contamination of eukaryotic DNA, that can easily be removed in the sequence processing. However, there are contamination of some sequences which are introduced by the DNA extraction kits and there are some studies related to this, and you can find out the most common contaminants.
Abhijeet Singh Thanks, I'm working with and eukaryotic endoparasite, in the first tryouts we found some contamination on the sequencing, even when we were working with a single specimen, but with some new procedures like another kind of washes, we solved it. But my question is more about when we find some sequences that "shouldn't" be there, for example, when working to find what species of fishes are there in someplace, and when you analyze, you find some human sequences, do you think this raises or lows the significance of the results, cause if you find this, what does it means, that your results are wrong or that it's so precise that found even other DNAs, or do you think its only a matter of primers and probes?
This problem can have several reasons, and since I don't know the details on analysis pipeline, I can't tell you much. But if you find the non-target sequences in your dataset, you should remove them. I don't think it changes the significance of your results. PCR amplicon based sequencing only gives information about the relative abundances, so the relative abundance will be the same if you remove your non-targets.
But to think about the root of the problem, please evaluate the marker, if it is unique in your target organism and how much similarity it shares to the human genes. Again, your reference database must only have the target group of your "FISH" and not human. In this way you might be able to only use the sequence which is of your interest. Again, please check for any contamination from human intervention.
Please update your conclusions/finding etc. related to your procedure and method later, when you are successful in your study. Would be interesting to know.
Abhijeet Singh I have some other questions on my page and a discussion where there is something that I think your opinion could really help me.
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