We have sequenced the same library twice. One for pair-end and another one for single-end. I have to remove PCR duplicates together since they are the same library. Can Picard handle this? Or is there any tools/methods I can try?
Please take a look at Article#6747 to see how MarkDuplicates handles PE and SE differently. The definition of what is a duplicate changes and so duplicates may be inflated for your SE reads. There is some discussion in the comments section on SE reads not allowing for optical duplicate detection that may interest you.
Let me know if you have questions.