Removals of duplicates before using circle-map

[MJoseMo]

I have a question regarding the handling of duplicate before running the software. I have read in other threads that it depends in the type of analysis we are interested in. In the case, we would like to perform a quantitative analysis. Is it advisable to remove PCR and optical duplicates or would it be enough eliminating optical ones ?

Any advice or suggestions would be greatly appreciated.

[iprada]

it highly depends o the research question as some things assume reads are independent. For circle map side, do not remove anything.

best,

Iñigo