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Hi everybody,
Various sources tell me it is not recommended to blindly discard all sequences flagged as chimeras by tools such as Chimera Slayer and UCHIME, and that you should manually check if they really represent PCR artifacts. Now I have been searching the literature as to how to do this but I can't seem to find an answer. Are there any tips as to how to further analyze putative chimeric sequences?
To clarify: We are talking about some 100 OTU representative sequences (16S bacterial pyrosequencing reads, approximately 250bp each) which remain unclassified at any level after alignment with SILVA, Greengenes, LTP, and RDP, and I want to dig deep as to whether these are PCR artifacts or possible new taxa (and not just rely on the UCHIME software).
Kind regards,
Sam
Various sources tell me it is not recommended to blindly discard all sequences flagged as chimeras by tools such as Chimera Slayer and UCHIME, and that you should manually check if they really represent PCR artifacts. Now I have been searching the literature as to how to do this but I can't seem to find an answer. Are there any tips as to how to further analyze putative chimeric sequences?
To clarify: We are talking about some 100 OTU representative sequences (16S bacterial pyrosequencing reads, approximately 250bp each) which remain unclassified at any level after alignment with SILVA, Greengenes, LTP, and RDP, and I want to dig deep as to whether these are PCR artifacts or possible new taxa (and not just rely on the UCHIME software).
Kind regards,
Sam
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