should we remove duplicates or just mark duplicates in the bam file for archR?

[YichaoOU]

Hello,

I have marked the duplicates per cell using picard. Will archR take care of these duplicates when reading the bam? Or I should remove the PCR duplicates before asking archR to process?

Thanks,
Yichao

[rcorces]

You should familiarize yourself with the bamFlag parameter which is used for this and similar filtering purposes