about remove duplicate

[transforu]

Hello!
I am having trouble about removing duplicate reads,
One experiment have many runs,
Should I remove duplicate one by one runs?
Or merge all runs then remove duplicate

Thanks for your help!

[dpryan]

Were the runs from the same library? If so, then merge and remove duplicates. If not, then remove duplicates and then merge. Duplicates need to be removed per library.

[transforu]

Very clear ! many thanks !!!