4 ms·

>Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Can you provide a source for this? There are a lot of cranks r

by tjpnz 4y ago

>Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Can you provide a source for this? There are a lot of cranks right now claiming that there's no such thing as a virus because we've never been able to get a non-contaminated sequence (something I've assumed was due to culturing). If this is true of everything there's no limit to what can and cannot exist per their insane arguments.

saurik 4y ago
Did you even try to look before throwing FUD? Into is really sketchy to me when people call for citations without noting at least in passing that they either found the opposite or tried something reasonable and failed to find something. In this case, I don't really know much about this either way, but 30 seconds of effort by just copy/pasting the exact sentence you quoted into Google found me something that seems to fit the bill, showing that contaminants in sequencing is "pervasive" and must be accounted for--such as by filtering things that look out of scope--to get reasonable results. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-0748-z https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-02... > Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability > We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling.
- tokai 4y ago
  You are using the term FUD incorrectly.
  - deleted 4y ago
    [deleted]
- throwaway290 4y ago
  The source is at least TFA published in Cell, axg11 discarded it without providing any. Thanks!

by tjpnz 4y ago

saurik 4y ago

Did you even try to look before throwing FUD? Into is really sketchy to me when people call for citations without noting at least in passing that they either found the opposite or tried something reasonable and failed to find something. In this case, I don't really know much about this either way, but 30 seconds of effort by just copy/pasting the exact sentence you quoted into Google found me something that seems to fit the bill, showing that contaminants in sequencing is "pervasive" and must be accounted for--such as by filtering things that look out of scope--to get reasonable results. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-0748-z https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-02... > Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability > We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling.

tokai 4y ago
You are using the term FUD incorrectly.
- deleted 4y ago
  [deleted]
throwaway290 4y ago
The source is at least TFA published in Cell, axg11 discarded it without providing any. Thanks!