Any downstream effect of setting OPTICAL_DUPLICATE_PIXEL_DISTANCE to 2500 for Patterned Flow Cell?
I used to work on data from NextSeq, so I don't need to
set OPTICAL_DUPLICATE_PIXEL_DISTANCE for MarkDuplicates.
Now I started to work on patterned flow cell data. I was
told that I should set OPTICAL_DUPLICATE_PIXEL_DISTANCE
I did that. I am getting higher optical duplicates and higher
library complexity from the MarkDuplicates metrics file.
However, there is no difference in the downstream files.
Is this expected? Or is there any way to generate better
Thanks a lot in advance.