Hello,
I am trying to find the best way to deal with PCR duplicates in ddRAD data. I was wondering if there is a reliable way to identify and exclude them in a dataset that has been produced without using degenerate adaptors.
Thank you very much in advance.
Did you use any UMI or MID during library prep? The only way to accurate de-dupe would be to "uniquely" label all your starting molecules with Molecular barcode (MID),.so you can track them after sequencing.
Yeah, you'll need a degenerate region added into your adapters if you want to filter PCR duplicates using traditional ddRAD. Without them, I guess the best approach is to just sequence at a high enough coverage so as to minimize the inclusion of PCR duplicated error into genotypes, and also minimizing the number of PCR cycles during library prep.
As far as I know, it is otherwise not possible to remove them post hoc bioinformatically, which as Sukhinder states can only be done with some sort of identifier (e.g. unique sequence in the degenerate region).
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