[ddRAD] on removal of duplicate reads

[skm]

Hi All,

Is it advisable to remove duplicate reads from double digest RAD (ddRAD) data generated on Illumina Hiseq platform ?

Regards,
Krishna

[nucacidhunter]

ddRAD libraries has two types of duplicates:

1- PCR duplicates
2- duplicates rising from input genome equivalent used for dig-lig

As most of ddRAD protocols does not use UMIs, it is not possible to distinguish those.

Throughout analysis a minimum coverage is used to form stacks of RAD-tags, catalog and estimate zygosity for the called genotypes so duplicates should not be removed.