Preprocessing circle-seq data before using circle-map

[Jiangxiaoyu1i]

Hello there,
I would like to ask, before processing the circle-seq data, your process is directly compared with bwa. I would like to ask whether to use picard to remove duplicates and merge samples for raw data.
Looking forward to your answer.
Good luck!
Jiang Xiaoyu

[iprada]

Dear Jiangxiaoyu1i,

I gave a similar answer in another thread. I copy-paste what I wrote:

This depends on the biological question you want to answer. If you are interested in a qualitative analysis where you only detect the circle keeping PCR duplicates is fine. If you want to do any quantitative analysis you should remove duplicates.

best,

Inigo