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Hi,
I am wondering the best approach for testing for contamination in short-read sequence data from host/environmental genomes which were not the target of the sequencing study. Specifically, I have mapped short read data to a reference genome and see an unexpected level of polymorphisms at the 16S locus. I would like to figure out if this variation is attributable to true biological variation, or potentially, if this variation is actually attributable to sequence reads from other contaminating genomes which map nevertheless to my reference genome of interest.
Thank you!
I am wondering the best approach for testing for contamination in short-read sequence data from host/environmental genomes which were not the target of the sequencing study. Specifically, I have mapped short read data to a reference genome and see an unexpected level of polymorphisms at the 16S locus. I would like to figure out if this variation is attributable to true biological variation, or potentially, if this variation is actually attributable to sequence reads from other contaminating genomes which map nevertheless to my reference genome of interest.
Thank you!
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