Keeping low number of PCR duplicates

[phoebe460]

Hi SICER2 Developers,

First off, thank you for creating a great peak calling tool. I am planning to use this for my own analysis for ChIP-seq data actually. In that case, I am wondering if there is a way to keep PCR duplicates using a --keep-duplicates flag, similar to what has been implemented in EPIC2 but setting it to just a low number for instance like 1, which would remove the majority of PCR duplicates found but still keep a low number of duplicates? I don't see a parameter that can do this under SICER2 arguments here.

A similar thing can be done using their keep duplicates flag in MACS3 as follows:

--keep-dup

It controls the MACS3 behavior towards duplicate tags at the exact same location – the same coordination and the same strand. You can set this as auto, all, or an integer value. The auto option makes MACS3 calculate the maximum tags at the exact same location based on binomial distribution using 1e-5 as p-value cutoff; and the all option keeps every tag. If an integer is given, at most this number of tags will be kept at the same location. The default is to keep one tag at the same location. Default: 1

If you can clarify this for me or even include a --keep-duplicates flag before I start using your program, then that would be greatly appreciated.

Thank you,
Phoebe