I use ddRADseq with DBR to deal with PCR duplicates. We basically add a DBR, in the Read2 paired end.
My questions are:
The references I base my protocol on are below:
Schweyen, H., Rozenberg, A., & Leese, F. (2014). Detection and removal of PCR duplicates in population genomic ddRAD studies by addition of a degenerate base region (DBR) in sequencing adapters. The Biological Bulletin, 227(2), 146–160.
Tin, M. M. Y., Rheindt, F. E., Cros, E., & Mikheyev, A. S. (2014). Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy. Molecular Ecology Resources, 15(2), 329–336.
My questions are:
- How can we deal with DBR bioinformatically? Is there a software that can deal with the DBRs?
- It seems that Stacks has different options to do this. If you go on their manual it seems that their Oligo sequence options for the clone_filter could do the trick. But it's unclear on how to apply it or if it's designed to deal with DBRs. Did someone used it before?
The references I base my protocol on are below:
Schweyen, H., Rozenberg, A., & Leese, F. (2014). Detection and removal of PCR duplicates in population genomic ddRAD studies by addition of a degenerate base region (DBR) in sequencing adapters. The Biological Bulletin, 227(2), 146–160.
Tin, M. M. Y., Rheindt, F. E., Cros, E., & Mikheyev, A. S. (2014). Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy. Molecular Ecology Resources, 15(2), 329–336.
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